Planta
2017 Jan 1;245(1):45-60. DOI: 10.1007/s00425-016-2590-7
Young Seedling Stripe1 encodes a chloroplast nucleoid-associated protein required for chloroplast development in rice seedlings
Zhou K. et al.,
1. National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingPeople’s Republic of China
2.National Key Laboratory for Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingPeople’s Republic of China
3.Rice Research InstituteAnhui Academy of Agricultural SciencesHefeiPeople’s Republic of China
... 1223 F 2 homozygous yss1 individuals (Fig. 4b). There are four open reading frames
(ORFs) in the segment and the genes were predicted using FGENESH 2.2
(http://www.softberry.com). Comparison with the wild-type genomic ...
New Phytologist
2017 Jan 1;213(2):916-28. DOI: http://dx.doi.org/10.1016/j.tube.2016.12.007
Rye B chromosomes encode a functional Argonaute?like protein with in vitro slicer activities similar to its A chromosome paralog
Ma W. et al.,
Universidad de Buenos Aires, Facultad de Agronomia, Catedra de Microbiologia Agricola.INBA-CONICET, Av. San Martin 4453, C1417DSE, Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Agronomia, Catedra de Microbiologia Agricola.INBA-CONICET, Av. San Martin 4453, C1417DSE, Buenos Aires, Argentina
... accession nos. ERP001061, PRJEB12520). The gene structure with putative intronic
and exonic regions was predicted by FGENESH (http://linux1.softberry.com/berry.
phtml) based on the A-located genes (Fig. S2). All GenBank ...
BMC Plant Biology
17(1), p.11. DOI: 10.1186/s12870-016-0964-4
Characterization of the sdw1 semi-dwarf gene in barley
Xu, Y. et al.,
Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University;
Western Barley Genetics Alliance, Murdoch University
... The exon and intron, and protein sequences of the HvGA20ox2 gene from each variety were identified by using BLASTN, TBLASTN, and
online gene prediction software FGENESH (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind). ...
International Journal of Agricultural Economics and Management
Volume 7, Number 1 (2017), pp. 7-16
In Silico Promter Prediction in Chromosome 10th of Sorghum Bicolor.
Mudgil D, Bhavika S, Singhal D.
Department of Biotechnology Engineering, Ambala College of Engineering and Applied Research, Ambala-134003, In
... The files of chromosome 10th (60.9 mb) were subjected to softberry software prediction(TSSP). ...
In this case loop was set in which 90 kb sized files were generated. Softberry: Based on fastest
and most accurate ab initio gene prediction program, FGENESH. ...
Journal of Basic Microbiology
2017 Feb 1. DOI: 10.1002/jobm.201600707
Effects of an alternative oxidase gene on conidia viability under external stresses in Monascus ruber M7
Shao Y, Li Q, Zhou Y, Chen F.
... All the isolated DNA fragments were sequenced and assembled using BLAST webserver
(http://blast.ncbi.nlm.nih.Gov/Blast.cgi). The Mraox protein sequence was deduced using
SoftBerry's FGENESH program (http://linuxl.softberry.com/berry.phtml). ...
Molecular Breeding
2017 Jan 1;37(1):3. doi:10.1007/s11032-016-0594-4
Tandem duplications of receptor-like kinase genes reshaped the homologous chromosome 1 regions in Oryza sativa ssp. indica and japonica and their possible ancestral genomes
Wang Z, Guo H, Cloutier S.
1.Cereal Research Centre, Agriculture and Agri-Food CanadaWinnipegCanada;
2.Chromatin Inc.LubbockUSA;
3.Plant Genome Mapping LaboratoryUniversity of GeorgiaAthensUSA;
4.Ottawa Research and Development Centre, Agriculture and Agri-Food CanadaOttawaCanada
... japonica gene sequences and renamed accordingly (Table S1). The O. glaberrima gene
annotation was similarly obtained (http://www.gramene.org) with the addition of a few new
genes annotated using FGenesH (http://linux1.softberry.com). ...
New Phytologist
2017 Jan 1;213(2):886-99. DOI: 10.1111/nph.14177
Divergent evolution of multiple virus?resistance genes from a progenitor in Capsicum spp.
Kim et al.,
Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea; Department of Horticulture, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, Korea
... net). The gene coding regions of the tomato scaffold were predicted using Fgenesh
(http://linux1.softberry.com). ... 2012). The gene coding regions of the tomato scaffold
were predicted using Fgenesh (http://linux1.softberry.com). ...
Developmental & Comparative Immunology
2017 Feb 28;67:464-70. http://dx.doi.org/10.1016/j.dci.2016.09.007
Analysis of apolipoprotein genes and their involvement in disease response of channel catfish after bacterial infection
Yang Y et al.,
The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
... 1e ?10 . The genes from retrieved sequences were predicted by FGENESH program
of Molquest software (Softberry Int.) and were further confirmed by BLASTP against
non-redundant (nr) protein database. Sequence analysis ...
Fish & Shellfish Immunology
2017 Jan 31;60:380-90. http://dx.doi.org/10.1016/j.fsi.2016.12.004
The chemokinome superfamily in channel catfish: I. CXC subfamily and their involvement in disease defense and hypoxia responses
Fu Q. et al.,
a State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China;
b The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
... with a cutoff E-value of 1e ?10 . Fgenesh program of Molquest software (Softberry
Int.) was used to predict the genes from retrieved genomic scaffold sequences [61].
The simple modular architecture research tool (SMART http ...
Developmental & Comparative Immunology
2017 Feb 28;67:166-76. http://dx.doi.org/10.1016/j.dci.2016.10.007
Intronless and intron-containing type I IFN genes coexist in amphibian Xenopus tropicalis: Insights into the origin and evolution of type I IFNs in vertebrates
Gan Z, Chen SN, Huang B, Hou J, Nie P.
a State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
b University of Chinese Academy of Sciences, Beijing, 100049, China
... Putative transcripts were predicted from the genome sequences using the GenScan
program (http://genes/mit.edu/GENSCAN.html) and the Fgenesh program
(www.softberry.com). 2.3. Cloning of intronless and intron-containing ...
Molecular Plant Pathology
2017 Jan 1;18(1):125-33. DOI: 10.1111/mpp.12467
A wheat COP9 subunit 5-like gene is negatively involved in host response to leaf rust
Zhang H, Wang X, Giroux MJ, Huang L.
Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA; State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shanxi, China
...The Softberry database (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind) was used for gene prediction. ...
Scientific Reports
2017; 7: 42596. doi: 10.1038/srep42596
TaWRKY70 transcription factor in wheat QTL-2DL regulates downstream metabolite biosynthetic genes to resist Fusarium graminearum infection spread within spike
Kage U, Yogendra KN, Kushalappa AC.
Plant Science Department, McGill University, 2111 Lakeshore road, Sainte Anne De Bellevue, Quebec, Canada, H9X3V9
... Contigs identified as the best hit for candidate genes were retrieved from database and the gene
prediction was performed using SoftBery–FGENESH (http://linux1.softberry.com/berry.phtml?
topic=fgenesh&group=programs&subgroup=gfind) program to study the gene structure. ...
International Journal for Parasitology
2017 Feb 10. http://dx.doi.org/10.1016/j.ijpara.2016.12.002
Comparative genomic analysis of the IId subtype family of Cryptosporidium parvum
Feng Y. et al.,
a College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
b State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
... Potential genes in major insertions were identified using FGENESH (http://www.softberry.
com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind) or geneid
(http://genome.crg.es/software/geneid/geneid.html) webservers. ...
Frontiers in Plant Science
2017 Jan 6;7:2019. https://doi.org/10.3389/fpls.2016.02019
Brassica juncea lines with substituted chimeric GFP-CENH3 give haploid and aneuploid progenies on crossing with other lines
Watts A. et al.,
1ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
2ICAR-Directorate of Medicinal and Aromatic Plants Research, Anand, India
... Secondary structure analysis of protein was done using Phyre2 and PSIPRED v3.3
softwares (Jones, 1999). FGENESH software (http://www.softberry.com/) was used to
predict the CENH3 transcript sequence from genomic sequence. ...
Scientia Horticulturae
2017 Feb 14;216:284-92. http://dx.doi.org/10.1016/j.scienta.2016.12.019
Identification and characterization of expressed TIR-and non-TIR-NBS-LRR resistance gene analogous sequences from radish (Raphanus sativus L.) de novo transcriptome
Wang Y. et al.,
a National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
b Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, PR China
... Gene identification and annotation were performed using FGENESH program
(http://www.softberry.com). The domain architecture of the predicted NBS-containing proteins
was verified with the Pfam ver 30.0 program (http://pfam.janelia.org). 2.3. ...
PloS one
2017 Feb 10;12(2):e0171291. http://dx.doi.org/10.1371/journal.pone.0171291
Phylogenomic analyses reveal the diversity of laccase-coding genes in Fonsecaea genomes
Moreno LF et al.,
CBS-KNAW Fungal Biodiversity Centre, Utrecht, Netherlands, Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands, Department of Basic Pathology, Federal University of Parana State, Curitiba, PR, Brazil; CBS-KNAW Fungal Biodiversity Centre, Utrecht, Netherlands, Department of Dermatology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Department of Basic Pathology, Federal University of Parana State, Curitiba, PR, Brazil
... laccases based on comparative analysis and crystallographic data (Table 3). The C-terminal
region of the laccase AYO21_07092 in F. monophora was found missing and its corresponding
genomic region was re-annotated by FGENESH 2.6 (http://www.softberry.com/) using ...
PloS one
2017 Feb 10;12(2):e0171111. http://dx.doi.org/10.1371/journal.pone.0171111
Role of N-linked glycosylation in the enzymatic properties of a thermophilic GH 10 xylanase from Aspergillus fumigatus expressed in Pichia pastoris
Chang X et al.,
College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China, Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
... The sequence assembly was performed using the Vector NTI Advance 10.0 software
(Invitrogen). Genes, introns, exons and transcription initiation sites were predicted using
the online software FGENESH (http://linux1.softberry.com/berry.phtml). ...
Theoretical and Applied Genetics
2017 Jan 16:1-5. doi:10.1007/s00122-016-2846-4
Brassica napus DS-3, encoding a DELLA protein, negatively regulates stem elongation through gibberellin signaling pathway
Zhao B et al.,
National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
... genes. Putative B. rapa, B. olera- cea and B. napus RGA sequences were
downloaded from these Brassica databases. Gene structures were predicted using
FGENESH (http://linux1.softberry.com/berry.phtml). Homology and ...
Plant Omics
2016, 9(4), p.248-260.
A computational study on genetic diversity of'shatterproof1 (shp1) and shatterproof2 (shp2)'genes in some members of'Oleraceae'and its molecular implications
Gahoi, S. et al.,
(1) National Bureau of Plant Genetic Resources, New Delhi-110012, India
(2) Centre for Agricultural Bioinformatics, ICAR-IASRI, Library Avenue, Pusa, New Delhi -110012, India
(3) National Bureau of Plant Genetic Resources, New Delhi-110012, India
... 2006). (http://www.softberry.com/berry.phtml?topic=fgenesh&group =programs&subgroup=gfind). ...
1 Determination of Exon/Intron structure FGENESH. (http://www.softberry.com/berry.phtml?topic=
fgenesh&group=programs&sub group=gfind) 2 Selection of Proteins for analysis ...
Tree Genetics & Genomes
2016, 12(6), p.120. doi:10.1007/s11295-016-1077-9
Development, evaluation, and validation of new EST-SSR markers in olive (Olea europaea L.)
Mariotti, R. et al.,
1. CNR-Institute of Biosciences and BioresourcesPerugiaItaly
2.CNR-Institute for Agricultural and Forest Systems in the MediterraneanPerugiaItaly
3.Department of Agricultural, Food and Environmental ScienceUniversity of PerugiaPerugiaItaly
... To predict the entire open reading frame (ORF) of each original transcript, genomic scaffolds
containing the target SSR regions were analyzed by Softberry FGENESH (http://linux1.softberry.
com) and were then functionally annotated by using the Blast2GO software (Conesa et al ...
Front Plant Sci.
2016; 7: 1775. 10.3389/fpls.2016.01775
Ca2+/cation antiporters (CaCA): Identification, characterization and expression profiling in bread wheat (Triticum aestivum L.)
Taneja, M., Tyagi, S., Sharma, S. and Upadhyay, S.K.
1 Department of Botany, Panjab University, Chandigarh, India
2 National Agri-Food Biotechnology Institute, Mohali, India
...The FGENESH pipeline (http://www.softberry.com/) was used for the prediction of coding sequence (Solovyev et al., 2006). ...
...The localization of the protein within the cell was predicted using
pSORT (http://wolfpsort.org/), CELLO v.2.5 (http://cello.life.nctu.edu.tw/), TargetP_v1, PredSL, ngLOC and
ProtComp (http://www.softberry.com/berry.phtml) ...
Journal of genetics
2016, 95(1), pp.177-181.
Characterization of two CYP77 gene family members related to development of ornamental organs in petunia
Yue, Y. et al.,
Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
... 2011). The full-length ORFs of Phcyp77A1 and Phcyp77B1 were predicted by the FGENESH
tool (http:// www.softberry.com) and amplified from the mixed flower buds cDNA template with
specific primers (table 1). All these primers were designed using Primer 5 software. ...
Angewandte Chemie
2016, 55(2), 664-678. DOI: 10.1002/ange.201509345
Identification and reconstitution of the polyketide synthases responsible for biosynthesis of the anti-malarial agent, cladosporin
Cochrane, R. V. et al.,
Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 (Canada)
Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
... Spliced gene sequences contained within this gene cluster were identified using the hidden
Markov model (HMM) based software FGENESH (Softberry),23 and the resulting intron-less
sequences were analyzed individually by BLAST (NCBI; Figure 1). Figure 1. Figure 1. ...
Gene
Volume 594, Issue 1, 5 December 2016, Pages 131–137 http://dx.doi.org/10.1016/j.gene.2016.08.058
A novel exon generates ubiquitously expressed alternatively spliced new transcript of mouse Abcc4 gene
Vivian et al.,
Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
... Different online tools used in our study are GENSCAN (http://genes.mit.edu/GENSCAN.html),
FGENESH (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=
gfind), FEX (http://linux1.softberry.com/berry.phtml?topic=fex&group ...
Molecular Genetics and Genomics
February 2017, Volume 292, Issue 1, pp 173–186 DOI: 10.1007/s00438-016-1265-1
Identification of candidate genes from the SAD gene family in cotton for determination of cottonseed oil composition
Shang, X., Cheng, C., Ding, J. and Guo, W.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of EducationNanjing Agricultural UniversityNanjingChina
... Further correction was performed by running gene prediction programs FGENESH (http://
www.softberry.com/berry.phtml) and SMART (http:// smart.embl-heidelberg.de/) to detect the
conserved motifs. ... dk/services/TargetP/) and ProtComp (http://www.softberry. ...
Insect Science
2016 28 Dec DOI: 10.1111/1744-7917.12415
Characterization of a laccase from a wood?feeding termite, Coptotermes formosanus
Geng, A. et al.,
Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
... The full open reading frame (ORF) was predicted using the online service of gene-structure
prediction by Softberry (FGENESH mode, http://www.softberry.com). Protein sequences were
aligned using Clustal X ver. 1.81 (Larkin et al., 2007). Vector construction. ...
Mycoscience
2016, 57(5), pp.320-325. http://dx.doi.org/10.1016/j.myc.2016.04.004
Further characterization of hydrophobin genes in genome of Flammulina velutipes
Kim, H.I., Lee, C.S. and Park, Y.J.
Department of Biomedical Chemistry, Konkuk University, Chungju 27478, Republic of Korea
... In our previous study, genome-wide identification of hydrophobin genes was carried out using
several methods, including ab initio gene structure prediction (Fgenesh; http://www.softberry.
com), a homology-based approach (Fgenesh+; http://www.softberry.com), and ...
Indian Journal of Medical Sciences
2016, 68(1), pp.49-53. http://dx.doi.org/10.18203/issn.0019-5359.IndianJMedSci20163531
NOVEL BIOINFORMATICS APPROACH DETECTS HUNDREDS OF PREVIOUSLY UNDETECTED SPLICED TRANSCRIPTS DISCOVERED FROM CAENORHABDITIS ELEGANS GENOME
Luv, K., Shrivastava, K., Shrivastava, A. and Chauhan, U.K.
... It is available at http://www.softberry.com/berry.phtml. ... It is available at http://genes.cse.wustl.edu/.
f. FGENESH[11] is also based on the Hidden Markov Model (HMM). It is available at
http://sun1.softberry. com/berry.phtml?topic=fgenesh&group=programs&su bgroup=gfind. ...
Insect Molecular Biology
2016 DOI: 10.1111/imb.12262
Ion transport peptide (ITP) regulates wing expansion and cuticle melanism in the brown planthopper, Nilaparvata lugens
Yu, B. et al.,
State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Science, Zhejiang University, Hangzhou, China
... The ORF regions of the detected ITP/ITPL transcripts were analysed using fgenesh
(http://linux1.softberry.com/berry.phtml?topic = fgenesh&group = programs&subgroup=gfind).
The 3' UTR, 5' UTR and ORF region of each N. lugens ITP/ITPL transcript were obtained. ...
BioMed Research International
2016 Article ID 7496569, 11 pages http://dx.doi.org/10.1155/2016/7496569
ChSte7 Is Required for Vegetative Growth and Various Plant Infection Processes in Colletotrichum higginsianum
Yuan, Q. et al.,
The Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei 430070, China
... All primers used in this work were designed with primer premier 5.0 (http://www.
premierbiosoft.com/primerdesign/). Open reading frames were further analyzed using the
gene prediction program FGENESH (Softberry Inc., Mount Kisco, NY, USA). ...
Theoretical and Applied Genetics
2016, DOI 10.1007/s00122-016-2752-9
The chlorophyll-deficient golden leaf mutation in cucumber is due to a single nucleotide substitution in CsChlI for magnesium chelatase I subunit
Gao, M., Hu, L., Li, Y., Weng, Y
1. College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
2. Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
... Gene annotation within this region was performed with FGENESH (http:// sunl.softberry.com/) and
function prediction was conducted with BLASTx at the NCBI website (http://blast.ncbi.nlm. ...
Fungal Genetics and Biology
2016, 92, 50-64. http://dx.doi.org/10.1016/j.fgb.2016.05.002
Construction of a genetic linkage map and analysis of quantitative trait loci associated with the agronomically important traits of Pleurotus eryngii
Im, C. H. et al.,
a Environment-friendly Research Division, Gyeongsangnam-do Agricultural Research and Extension Services, Jinju, Republic of Korea
b Department of Horticultural Bioscience, Pusan National University, Milyang, Republic of Korea
c US Forest Products Laboratory, Madison, WI, USA
... LOD and R 2 score) was obtained using a P. eryngii genome browser
(http://112.220.192.2/per/) and analyzed using the FGENESH (http://www.softberry.com/), UniProt ...
Developmental & Comparative Immunology
2016, 65, 268-279. http://dx.doi.org/10.1016/j.dci.2016.07.018
Identification of a fourth ancient member of the IL-3/IL-5/GM-CSF cytokine family, KK34, in many mammals
Yamaguchi, T., Schares, S., Fischer, U., & Dijkstra, J. M.
a Laboratory of Fish Immunology, Institute of Infectology, Friedrich-Loeffler-Institut, Sudufer 10, Greifswald-Insel Riems 17493, Germany
b Institute for Comprehensive Medical Science, Fujita Health University, Dengakugakubo 1-98, Toyoake, Aichi 470-1192, Japan
... were made based on using the specialized software GENSCAN,
http://genes.mit.edu/GENSCAN.html, and FGENESH, http://www.softberry.com/berry ...
New Phytologist
2016 DOI: 10.1111/nph.14110
Rye B chromosomes encode a functional Argonaute?like protein with in vitro slicer activities similar to its A chromosome paralog
Ma, W. et al.,
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
Institute of Bioinformatics and Systems Biology/Munich Information Center for Protein Sequences, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
National Bioinformatics Infrastructure Sweden, Department of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
... The gene structure with putative intronic and exonic regions was
predicted by FGENESH (http://linux1.softberry.com/berry.phtml) based on the A-located ...
Fungal Genetics and Biology
2016, 87, 54-63 http://dx.doi.org/10.1016/j.fgb.2015.12.013
MAT–gene structure and mating behavior of Hymenoscyphus fraxineus and Hymenoscyphus albidus
Wey, T., Schlegel, M., Stroheker, S., Gross, A.
Forest Pathology and Dendrology, Institute of Integrative Biology (IBZ), ETH Zurich, Universitatsstrasse 16, 8092 Zurich, Switzerland
... The gene prediction tool FGENESH (http://linux1.
softberry.com/berry.phtml) was used for the Botryotinia fuckeliana or Sclerotinia sclerotiorum-
specific gene-finding parameters to identify genes on the additional sequence fragment. ...
Fish & Shellfish Immunology
2016, 56, 70-83. http://dx.doi.org/10.1016/j.fsi.2016.06.049
Molecular and functional characterization of Toll-like receptor (Tlr) 1 and Tlr2 in common carp (Cyprinus carpio)
Fink, I. R. et al.,
a Cell Biology and Immunology Group, Department of Animal Sciences, Wageningen University, PO Box 338, 6700 AH, Wageningen, The Netherlands
b Department of Infectious Diseases and Immunology, Utrecht University, Yalelaan 1, 3584 CL, Utrecht, The Netherlands
... Exon-intron structure was studied by multiple alignments and open reading frame
predictions (FGENESH at http://linux1.softberry.com/berry.phtml?topic=fgenesh&group ...
Chromosome Research
2016, 24(2), 197-216. DOI: 10.1007/s10577-015-9515-3
Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis
Iwata-Otsubo, A., Lin, J. Y., Gill, N., Jackson, S. A.
Center for Applied Genetic TechnologiesUniversity of Georgia
Department of BiologyUniversity of Pennsylvania
... 1998; Gordon
et al. 1998). FGENESH (www.?softberry.?com/?) was used for de novo gene prediction. ...
Frontiers in plant science
2016, 7: 284. doi: 10.3389/fpls.2016.00284
Diverse evolutionary trajectories for small RNA biogenesis genes in the oomycete genus Phytophthora
Bollmann, S. R., Fang, Y., Press, C. M., Tyler, B. M., Grunwald, N. J.
1Horticultural Crop Research Unit, USDA-Agricultural Research Service, Corvallis, OR, USA
2Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, USA
.. homologs were isolated and coding sequences were manually identified or confirmed using
Genscan (Burge and Karlin, 1997) or FGENESH (linux1.softberry.com/berry ... in-frame fused with
GFP by inserting into the blunt site Stu I in the plasmid pYF2-GFP (Fang and Tyler, 2016). ...
Frontiers in genetics
2016, 7: 38. doi: 10.3389/fgene.2016.00038
Microsomal omega-3 fatty acid desaturase genes in low linolenic acid soybean line RG10 and validation of major linolenic acid QTL
Reinprecht, Y., & Pauls, K. P.
Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
... The gene structure was also analyzed
with the FGenesh 2.6 (http://linux1.softberry.com; Salamov and Solovyev, 2000). ...
Front. Plant Sci
08 August 2016 7, 1140. | http://dx.doi.org/10.3389/fpls.2016.01140
Analysis of Magnaporthe oryzae Genome Reveals a Fungal Effector, Which Is Able to Induce Resistance Response in Transgenic Rice Line Containing Resistance Gene, Pi54
Ray, S. et al.,
1National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
2Chaudhary Sarwan Kumar Himachal Pradesh Agricultural University, Palampur, India
... The supercontigs obtained after assembling the sequence reads were used for gene prediction using
FGENESH 8 taking Magnaporthe as reference database for gene prediction. ...
Developmental & Comparative Immunology
2016, 61, 208-224. http://dx.doi.org/10.1016/j.dci.2016.04.004
Evolution of IFN-? in tetrapod vertebrates and its functional characterization in green anole lizard (Anolis carolinensis)
Chen, S. N. et al.,
a State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
b University of the Chinese Academy of Sciences, Beijing 10049, China
... Putative transcripts were predicted from the lizard genome
sequences using the FGENESH program (http://linux1.softberry.com/berry.phtml). ...
Current Biotica
9(4):306-312, 2016
Expression profiling of anthocyanin pathway genes in popular tomato cultivars of India
Aumreetam Dinabandhu and Bidya Bhushan Gupta
ICAR-National Research Center on Plant Biotechnology, Pusa Campus, New Delhi-110 012, India
#Present address: Department of Biotechnology, Indian Institute of Technology, Roorkee –
247 667, Haridwar dt., Uttarakhand, India
... sequence of International Tomato Annotation Group release was used from http://solgenomics.
net/ and anthocyanin genes were predicted by using BLAST- Basic Local Alignment Search Tool
(http://blast.ncbi.nlm.nih.gov/ Blast.cgi) and FGENESH (www.softberry.com) gene ...
Applied Biochemistry and Biotechnology
2016 doi:10.1007/s12010-016-2164-y
Cloning and Expression Analysis of Eight Upland Cotton Pentatricopeptide Repeat Family Genes
Han, Z. et al.,
Cotton Research Centre Shandong Academy of Agricultural Sciences; School of Biological Science and TechnologyUniversity of Jinan
... Potential genes of the retrieved bacterial artificial chromosome (BAC) sequences were predicted
by a program FGENESH (http://www.softberry.com/), and the predicted proteins were used
subsequently as input for BLASTP searches against the non- redundant GenBank protein ...
Functional & integrative genomics
July 2016, Volume 16, Issue 4, pp 429-439 doi:10.?1007/?s10142-016-0494-z
Structural organization of fatty acid desaturase loci in linseed lines with contrasting linolenic acid contents
Thambugala, D., Ragupathy, R., Cloutier, S.
1. Department of Plant Science, University of Manitoba, 66 Dafoe Rd, Winnipeg, MB, R3T 2N2, Canada
2. Ottawa Research and Development Centre, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
.. Gene annotation. Gene prediction algorithm of FGENESH
(http://?www.?softberry.?com/?) and the previously predicted ab initio gene sequences of the
WGS sequence of CDC Bethune were further verified using FLAX GFF3 (Wang et al. ...
The Plant Journal
2016 DOI: 10.1111/tpj.13214
Rapid evolutionary dynamics in a 2.8?Mb chromosomal region containing multiple prolamin and resistance gene families in Aegilops tauschii
Dong, L. et al.,
United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, California
Department of Plant Sciences, University of California, Davis, CA, USA
... In addition, FGENESH (http://www.softberry
.com/nucleo.html), GeneMark, and GeneScan were used for gene prediction. ...
Journal of Bioscience and Bioengineering
2016 doi:10.1016/j.jbiosc.2016.05.003
Heterologous production of an acidic thermostable lipase with broad-range pH activity from thermophilic fungus Neosartorya fischeri P1
Sun, Q. et al.,
1 Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
2 Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Bioengineering, Tianjin University of Science & Technology, Tianjin 300457, PR China
... strand of cDNA
as template, the exon-intron boundaries were predicted using the online software GENSCAN
(http://genes.mit.edu/GENSCAN.html) and FGENESH (http://www.softberry.com/berry ...
Scientific reports
2016, 6: 25107. doi: 10.1038/srep25107
Comprehensive analysis of the polygalacturonase and pectin methylesterase genes in Brassica rapa shed light on their different evolutionary patterns
Duan, W. et al.,
1State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
2Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
... splicing errors, and missed or extra exons, manual
reannotation was performed using the FGENESH program (http://linux1.softberry.com/berry ...
Applied and environmental microbiology
2016, 82(4), 1196-1204. doi: 10.1128/AEM.03168-15
A fivefold parallelized biosynthetic process secures chlorination of Armillaria mellea (honey mushroom) toxins
Wick, J. et al.,
aDepartment of Pharmaceutical Microbiology, Hans Knoll Institute, Friedrich-Schiller-Universitat Jena, Jena, Germany
bDepartment of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoll Institute, Jena, Germany
... for 3 min. In silico sequence and phylogenetic analysis.To identify exon-intron
junctions in silico, we used FGENESH (Softberry, Mount Kisco, NY) and Augustus
(26) software as described previously (27). Primary sequences ...
The Plant Genome
2016 doi:10.3835/plantgenome2015.09.0084
Fine Mapping of Two Wheat Powdery Mildew Resistance Genes Located at the Pm1 Cluster
Liang, J. et al.,
a The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
b current address, Crop Research Institute, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
... Gene prediction was performed using the gene predictor
program FGENESH (http://www.softberry.com) complemented with BLASTn search against dbEST ...
Frontiers in Plant Science
2016, 7: 967. doi: 10.3389/fpls.2016.00967
HyPRP1 Gene Suppressed by Multiple Stresses Plays a Negative Role in Abiotic Stress Tolerance in Tomato
Li, J. et al.,
1Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education; College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
2Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, China
... Both SlHyPRP1 and SpHyPRP1 encoded 262 amino
acids predicted by the FGENESH program (http://linux1.softberry.com/berry.phtml). ...
Theoretical and Applied Genetics
2016, 1-12. DOI: 10.1007/s00122-016-2740-0
The Solanum demissumR8 late blight resistance gene is an Sw-5 homologue that has been deployed worldwide in late blight resistant varieties
Vossen, J. H. et al.,
Wageningen UR Plant BreedingWageningen University and Research
... Gene structures
were predicted using FGENESH 2.6(Softberry) and protein sequences were deduced
by translation of ORF using the standard genetic code. ...
Plant, Cell & Environment
2016 DOI: 10.1111/pce.12779
Different cytokinin histidine kinase receptors regulate nodule initiation as well as later nodule developmental stages in Medicago truncatula
Boivin, S. et al.,
... Prediction of gene structures using FGENESH (http://linux1.softberry.
com/) revealed that the MtCHK1/MtCRE1 transcript contains 11 predicted exons ...
G3: Genes| Genomes| Genetics
2016, 6(5), 1179-1189. doi: 10.1534/g3.115.026229
Sequence of the Gonium pectorale Mating Locus Reveals a Complex and Dynamic History of Changes in Volvocine Algal Mating Haplotypes
Hamaji, T. et al.,
*Donald Danforth Plant Science Center, St Louis, Missouri 63132
†Department of Biological Sciences, Graduate School of Science, University of Tokyo 113-0033, Japan
‡Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721
... Gene models were generated using Fgenesh (Salamov and Solovyev 2000) (http://linux1.softberry.
com/berry.phtml) with the “Chlamydomonas” option, and then manually edited based on similarity
to C. reinhardtii (JGI V4 protein models: http://genome.jgi-psf.org/Chlre4 ... 2016). ...
Biotechnology for Biofuels
2016 9:147 DOI: 10.1186/s13068-016-0560-8
Engineering a highly active thermophilic ?-glucosidase to enhance its pH stability and saccharification performance
Xia, W. et al.,
Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences
College of Animal Science, Zhejiang University
... Genes, introns, exons and transcription initiation sites were predicted using the online software
FGENESH (http://linux1.softberry.com/berry.phtml). ...
PloS one
2016, 11(3), e0150988. DOI: 10.1371/journal.pone.0150988
Missed, not missing: Phylogenomic evidence for the existence of Avian FoxP3
Denyer, M. P., Pinheiro, D. Y., Garden, O. A., Shepherd, A. J.
Department of Clinical Sciences and Services, The Royal Veterinary College, London, United Kingdom, Institute of Structural and Molecular Biology and Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom
Institute of Structural and Molecular Biology and Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom
... Gene prediction software such as Softberry FGENESH [41] still predicts that
foxp3 is present in the inter-genic region between ppp1r3f and ccdc22 (S1 File). ...
Immunogenetics
2016, 68(1), 77-82. DOI: 10.1007/s00251-015-0885-7
Assembly and characterization of the MHC class I region of the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis)
Ruan, R., Wan, X. L., Zheng, Y., Zheng, J. S., Wang, D.
1. Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
2. University of Chinese Academy of Sciences, Beijing, 100039, China
... KP994094. First, Genscan (http://genes.mit.edu/GENSCAN.html) and Fgenesh
(http://www.softberry.com/) (Burge and Karlin 1997; Salamov and Solovyev 2000) were
used to predict genes pre- senting in the YFP MHC class I region. ...
Molecular Genetics and Genomics
2016, 291: 1137–1154. doi:10.1007/s00438-016-1169-0
Genome-wide analysis of CrRLK1L gene family in Gossypium and identification of candidate CrRLK1L genes related to fiber development
Niu, E. et al.,
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of EducationNanjing Agricultural University
...he CrRLK1L sequences were obtained after being confirmed by the online FGENESH
(http://www.softberry.com/berry. phtml; Solovyev et al. 2006) and SMART (http://smart. ...
Plant biotechnology journal
2016 DOI: 10.1111/pbi.12577
Identification and molecular characterization of the nicotianamine synthase gene family in bread wheat
Bonneau, J., Baumann, U., Beasley, J., Li, Y., Johnson, A. A.
School of BioSciences, The University of Melbourne, Melbourne, Vic., Australia
Australian Centre for Plant Functional Genomics, The University of Adelaide, Adelaide, SA, Australia
... genes. Matching sequences from the IWGSC portal were annotated using the TriAnnot-v1.4
(http://wheat-urgi.versailles.inra.fr) and FGENESH (http://www.softberry.com/) pipelines ...
South African Journal of Botany
2016, 102, 142-152. doi:10.1016/j.sajb.2015.06.012
YUCCA type auxin biosynthesis genes encoding flavin monooxygenases in melon: Genome-wide identification and developmental expression analysis.
Zheng, L. et al.,
a Forestry and Fruit Research Institute, Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
b School of Life Sciences, Taizhou University, Taizhou, Zhejiang 317000, China
... Thereafter, HMM-based gene structure prediction was carried out using the FGENESH
program (default values) at http://linux1.softberry.com/berry.phtml. ...
Journal of insect physiology
2016, 58(4), 570-579. doi:10.1016/j.jinsphys.2011.12.009
Localization of two Na+-or K+-H+ antiporters, AgNHA1 and AgNHA2, in Anopheles gambiae larval Malpighian tubules and the functional expression of AgNHA2 in yeast
Xiang, M. A., Linser, P. J., Price, D. A., & Harvey, W. R.
a Division of Nephrology and Hypertension, Department of Medicine, University of Florida-Jacksonville, Jacksonville, FL 32206, USA
b Whitney Mosquito Biology Group, University of Florida, 9505 Ocean Shore Boulevard, St. Augustine, FL 32080, USA
... gambiae
that were applied to FGENESH at the Softberry site (http://www.softberry.com/berry.phtml) identified
a cDNA from a genomic region of ?30 kb; it included the originally predicted ...
Tree Genetics & Genomes
2016, 12: 2. DOI: 10.1007/s11295-015-0962-y
Homologs of the FB_MR5 fire blight resistance gene of Malus? robusta 5 are present in other Malus wild species accessions
Wohner, T et al.,
Julius Kuhn-Institut, Institute for Breeding Research on Fruit Crops,
Medical Theoretical Center (MTZ), Experimental Center, Faculty of Medicine Carl Gustav CarusTechnical University Dresden
... Gene and protein predictions were made with FGENESH (www.?softberry.?com)
using the organism-specific parameters for Solanum lycopersicum. ...
Theoretical and Applied Genetics
2016, 129(3), 507-516. DOI: 10.1007/s00122-015-2644-4
Fine mapping of a dominantly inherited powdery mildew resistance major-effect QTL, Pm1.1, in cucumber identifies a 41.1 kb region containing two tandemly arrayed cysteine-rich receptor-like protein kinase genes
Xu, X. et al.,
1. School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
2. USDA-ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
... al. 2012). Gene prediction and sequence annotation The genomic DNA region
harboring the PMR locus was annotated with FGENESH (http://sunl.softberry.com/)
and InterProScan (http://www.ebi.ac.uk/InterProScan). Genes ...
Theoretical and Applied Genetics
2016, 129(1), 53-64. DOI: 10.1007/s00122-015-2608-8
Map-based cloning reveals the complex organization of the BnRf locus and leads to the identification of BnRf b, a male sterility gene, in Brassica napus
Deng, Z. et al.,
1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
2. Institute of Crop Science, Anhui Academy of Agricultural Science, Hefei, 230031, China
.. Bioinformatics analysis The website-based software FGENSH (http://www.soft- berry.com)
was used to predict putative ORFs from the candidate region. The genomic or coding
sequences of predicted genes were submitted to NCBI (http://www. ...
Crop and Pasture Science
2016, 67(5), 541-552. doi: 10.1071/CP15165
NB-LRR gene family required for Rsc4-mediated resistance to Soybean mosaic virus
Li, N. et al.,
National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang 1, Nanjing 210095, P.R. China.
... The online program Fgenesh
(www.softberry.com/) was used to predict open reading frames (ORFs). ...
Sci Rep.
2016; 6: 29072. doi: 10.1038/srep29072
Expansion of amphibian intronless interferons revises the paradigm for interferon evolution and functional diversity
Sang, Y. et al.,
Departments of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, USA
2Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, USA
3Arthropod-Borne Animal Diseases Research Unit, Center for Grain and Animal Health Research, Agricultural Research Service, United States Department of Agriculture, Manhattan, KS, USA
...Programs interactively used for gene prediction include GenomeScan (http://genes.mit.edu/genomescan.html)
and FGENESH (http://www.softberry.com), and were further manually annotated for confirmation. ...
... Regulatory elements in the putative proximal promoters were examined against both human/animal TFD Database using program Nsite (Version 5.2013, at http://www.softberry.com)39. ...
Insect molecular biology
Volume 25, Issue 3 June 2016 Pages 191–201 DOI: 10.1111/imb.12210
The transformer genes in the fig wasp Ceratosolen solmsi provide new evidence for duplications independent of complementary sex determination
Jia, L. et al.,
Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, China
... local BLAST searches (Altschul
et al., 1990) using previously published protein sequences of Tra from closely related species
and predicted gene structures with FGENESH1 in the SOFTBERRY software package (ht ...
Environmental and Experimental Botany
2016, 121, 121-131. doi:10.1016/j.envexpbot.2015.05.016
FTL2 expression preceding bud set corresponds with timing of bud set in Norway spruce under different light quality treatments
Opseth, L. et al.,
Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 As, Norway
... 2.6. Phylogenetic analysis. The coding DNA
sequences of the PaPHYs and PaCRYs were translated into protein using GENSCAN
(http://genes.mit.edu/GENSCAN.html) and FGENESH (http://sun1.softberry.com/berry.phtml). ...
Fungal Biology
2016 doi:10.1016/j.funbio.2016.06.005
Cytochrome P450 complement (CYPome) of Candida oregonensis, a gut-associated yeast of bark beetle, Dendroctonus rhizophagus
Hernandez-Martinez, F., Briones-Roblero, C. I., Nelson, D. R., Rivera-Orduna, F. N., & Zuniga, G.
a Departamento de Zoologia, Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Prolongacion de Carpio y Plan de Ayala, Col. Sto. Tomas, Mexico D.F. CP 11340, Mexico
b Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Ave. Suite G01, Memphis, TN 38163, USA
... in both processes have been documented (DiGuistini et al., 2011, Adams et al., 2013, Lah et
al., 2013 and Xu et al., 2016). ... based (HMM) gene structure prediction was performed using the
Fgenesh program (Solovyev 2007) in the MolQuest package v 2.4.5.1135 (SoftBerry Inc. ...
Microbiological Research
2016, 192, 142-147. doi:10.1016/j.micres.2016.06.010
Identification of genes associated with asexual reproduction in Phyllosticta citricarpa mutants obtained through Agrobacterium tumefaciens transformation
Goulin, E. H. et al.,
a Department of Genetics, Universidade Federal do Parana, P.O. BOX 19071, CEP: 81531-980 Curitiba, PR, Brazil
b Fund for Citrus Protection, Fundecitrus, Av. Dr. Adhemar Pereira de Barros, 201, CEP: 14807-040 Araraquara, SP, Brazil
... in which the T-DNA insertion was located were
selected for gene prediction using FGENESH software (http://www.softberry.com/berry ...
PloS one
2016, 11(1), e0147486. doi: 10.1371/journal.pone.0147486
Two Horizontally Transferred Xenobiotic Resistance Gene Clusters Associated with Detoxification of Benzoxazolinones by Fusarium Species
Glenn, A. E. et al.,
USDA, ARS, Richard B. Russell Research Center, Toxicology & Mycotoxin Research Unit, Athens, Georgia, United States of America
University of Georgia, Department of Plant Pathology, Athens, Georgia, United States of America
... Manual
annotation of cluster genes was done by comparison to F. verticillioides and other annotated
species and by using FGENESH [29] through www.softberry.com. ...
PloS one
2016, 11(7), e0160197. doi: 10.1371/journal.pone.0160197
Identification of Novel Transcribed Regions in Zebrafish (Danio rerio) Using RNA-Sequencing
Wang, J., Vesterlund, L., Kere, J., Jiao, H.
Department of Biosciences and Nutrition, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
Clinical Research Centre, Karolinska University Hospital, Huddinge, Sweden
... Besides using junction information to clarify hypothetical exon
boundaries within clusters, we also used gene models provided by GENSCAN [16] and open
reading frame (ORF) predicted using FGENESH software (http://www.softberry.com) to ...
Mycoscience
2016, 57(2), 136-143 doi:10.1016/j.myc.2015.12.003
Cloning and characterization of cuticle-degrading serine protease from nematode-trapping fungus Arthrobotrys musiformis
Tzean, Y. et al.,
a Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei 10617, Taiwan, ROC
b Department of Energy, Plant Research Laboratory, Michigan State University, East Lansing, MI 48824-1312, USA
... The
5?UTR was predicted using Softberry FGENESH gene prediction software. ...
Theoretical and Applied Genetics
2016, 129(2), 305-316. DOI: 10.1007/s00122-015-2628-4
Identification and mapping of Tril, a homeodomain-leucine zipper gene involved in multicellular trichome initiation in Cucumis sativus
Wang, Y. L. et al.,
1. School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
2. Hunan Vegetable Research Institute, Hunan Academy of Agriculture Sciences, Changsha, 410125, China
... The functions of candi- date genes were retrieved from the NCBI website (http:// archive-dtd.ncbi.
nlm.nih.gov/). According to dicot plant (Arabidopsis)-based gene structure prediction (http://
linux1.softberry.com/), the Cucsa.045360 gene structure was identified in the tril mutant. ...
Genome biology and evolution
2016, 8(2), 302-316. doi: 10.1093/gbe/evv259
Retention, Molecular Evolution, and Expression Divergence of the Auxin/Indole Acetic Acid and Auxin Response
Factor Gene Families in Brassica Rapa Shed Light on Their Evolution Patterns in Plants
Huang, Z. et al.,
1State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture of Nanjing Agricultural University, Nanjing, P.R. China
2Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
... Then, the FGENESH program (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=
programs&subgroup=gfind) was used to rectify incorrect start codon predictions, splicing errors,
and missed or extra exons; manual reannotation was performed. ...
Genes & Genomics
2016, 38(2), 109-117. DOI: 10.1007/s13258-015-0356-4
Identification and evolutionary history of the DD41D transposons in insects
Zhang, H. H., Shen, Y. H., Xiong, X. M., Han, M. J., Zhang, X. G.
1. College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
2. State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
... Potential open reading frame (ORF) of rosa and Lsra transposons identified in this study was
predicted using FGENESH (http://?linux1.?softberry.?com/?berry.?phtml), GENSCAN
(http://?genes.?mit.?edu/?GENSCAN.?html) or getorf in EMBOSS-6.3.1 package (Rice et al. ...
Mycologia
2016, 15-200. doi: 10.3852/15-200
mrskn7, a putative response regulator gene of Monascus ruber M7, is involved in oxidative stress response, development and mycotoxin production
Shao, Y., Yang, S., Zhang, Z., Zhou, Y., Chen, F.
1 Huazhong Agricultural University, Wuhan, Hubei
3Hubei Academy of Agricultural Sciences, Wuhan, Hubei
4Huazhong Agricultural University, Wuhan, Hubei, 430070, China
... BLAST webserver (http://blast.ncbi.nlm.nih.Gov/Blast.cgi). The mrskn7 protein sequence
was deduced using SoftBerry's FGENESH program (http://linuxl.softberry.com/berry.
phtml). Homology analysis was subsequently performed ...
Plant Cell Reports
2016, 1-12. DOI: 10.1007/s00299-016-2008-9
Reduction of GIGANTEA
Kim, J. A. et al.,
1. Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 370, Nongsaengmyeong-ro, Wansan-gu, Jeollabuk-do, Jeonju-si, 560-500, Korea
2. Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755-3563, USA
.. A bacterial artificial chromosome (BAC) clone containing the ortholog of GI was identified
(http://www.brassica-rapa.org), and the GI structure and sequence were predicted using the
web-based gene prediction software FGENE-SH Arabidopsis (http://www.softberry.com/berry ...
Genetica
2016, 144(2), 229-241. DOI: 10.1007/s10709-016-9893-2
Comparative analysis of genome-wide Mlo gene family in Cajanus cajan and Phaseolus vulgaris
Deshmukh, R., Singh, V. K., Singh, B. D.
1. Faculty of Science, School of Biotechnology, Banaras Hindu University, Varanasi, 221005, India
2. Faculty of Science, Centre for Bioinformatics, School of Biotechnology, Banaras Hindu University, Varanasi, 221005, India
... The Fgenesh (http://linux1.softberry.com/) and GENSCAN (http://genes.mit.edu/; Burge and Karlin
1997) online ser- vers were used to detect/confirm the Mlo gene structures and the positions
of transcription start sites and polyA tails in the Mlo members from the two species. ...
Gene
2016, 585(2), 196-204. doi:10.1016/j.gene.2016.02.034
Identification and evolution of two insulin receptor genes involved in Tribolium castaneum development and reproduction
Sang, M., Li, C., Wu, W., Li, B.
Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
... http://beetlebase.org) (Kim et al., 2010). The initial search results were further
analyzed using the gene prediction software FGENESH (http://linux1.softberry.com/
berry.phtml). Based on the predicted sequences, we designed ...
PloS one
2016, 11(3), e0151323. http://dx.doi.org/10.1371/journal.pone.0151323
An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry
Dhanyalakshmi, K. H. et al.,
Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru, 560065, India National Centre for Biological Sciences, TIFR, GKVK campus, Bengaluru, 560065, India
... The gene prediction was carried out using available online tools like Softberry's HMM-based
ab-initio gene structure prediction by FGENESH [15] with Populus trichocarpa as reference
genome and AUGUSTUS (A. thaliana), a HMM-based eukaryotic gene prediction server [16 ...
Scientific reports
2016, 6: 25591. doi: 10.1038/srep25591
Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species
Zhong, Z. et al.,
1Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
2Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
... Gene predictions was conducted through a combination of evidence-based prediction by
Exonerate 58 (version 2.2.0) with M. oryzae 70-15 genes as reference and de novo prediction
with Fgenesh from SoftBerry (http://linux1.softberry.com/berry.phtml) with Magnaporthe as ...
Genetics and molecular research: GMR
2016, 15(1). DOI http://dx.doi.org/10.4238/gmr.15017507
Regulation of bolting and identification of the ?-tubulin gene family in Brassica rapa L. ssp pekinensis
Zhang, Y. W. et al.,
1 College of Horticulture, Northeast Agricultural University, Harbin, China
2 Key Laboratory of Biology and Genetic Improvement of Horticultural Crops
(Northeast Region), Ministry of Agriculture, Harbin, China
... Each TUA gene loci in A. thaliana was used to search all the TUA gene sequences of B.
rapa present in BRAD. Each predicted B. rapa TUA gene sequence was confirmed using
FGENESH (http://www.softberry.com/berry.phtml?topic=fgenesh). ...
Brazilian journal of microbiology
2016, 47(2), 468-479. http://dx.doi.org/10.1016/j.bjm.2016.01.004
Isolation and expression of two polyketide synthase genes from Trichoderma harzianum 88 during mycoparasitism
Yao, L. et al.,
aKey Laboratory of Molecular and Cytogenetics and Genetic Breeding of Heilongjiang Province, Harbin Normal University, Harbin, PR China
bDepartment of Life Science and Engineering, Harbin Institute of Technology, Harbin, PR China
... http://www.phrap.org/). The potential open reading frames (ORFs) of the two PKSs
were scanned using FGENESH as the matrix (http://linux1.softberry.com) and
compared with T. virens gene sequences. The conserved PKS ...
heoretical and Applied Genetics
2016, Volume 129, Issue 7 , pp 1247-1256 DOI: 10.1007/s00122-016-2700-8
Map-based cloning, identification and characterization of the w gene controlling white immature fruit color in cucumber (Cucumis sativus L.)
Liu, H. et al.,
1. College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
... Sequence analyses Gene prediction was performed using the online program FGENESH
(http://linux1.softberry.com/berry.phtml) (Salamov and Solovyev 2000) and Cucumber
Genome Browser (http://www.icugi.org/cgi-bin/ICuGI/index.cgi). ...
Biotechnology letters
2016, 38(1), 71-79. DOI: 10.1007/s10529-015-1943-9
Characterization of a farnesyl diphosphate synthase gene from Penicillium brevicompactum MUCL 19011
Sharifirad, A. et al.,
1. Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
... www.?genomatix.?de/?cgi-bin/?eldorado/?main.?pl ). ORF features were predicted
using the web-based software FGENESH (http://?linux1.?softberry.?com/?berry.?
phtml). The PbFDS was subjected to multiple alignments ...
Heredity
116, 491-501 (June 2016) | doi:10.1038/hdy.2016.5
The cacao pathogen Moniliophthora roreri (Marasmiaceae) possesses biallelic A and B mating loci but reproduces clonally
Diaz-Valderrama, J. R., Aime, M. C.
Institute
... In addition, the genomic surrounding areas of receptors were explored to find linked potential
B pheromone precursor sequences by manually identifying the conserved motifs (Riquelme et
al., 2005) in small polypeptides detected by FGENESH (http://www.softberry.com/). ...
Frontiers in plant science
2016, 7: 244. doi: 10.3389/fpls.2016.00244
Functional characterization of novel chitinase genes present in the sheath blight resistance QTL: qSBR11-1 in rice line Tetep
Richa, K. et al.,
1 ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
2 Department of Bioscience and Biotechnology, Banasthali Vidyapith, Vanasthali, India
3 School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
... Computational analysis of the genes. Full length nucleotide sequence of 11 defense response
genes was retrieved from the rice genome database (www.gramene.org). FGENESH gene
prediction software (www.softberry.com) was used to predict the candidate gene structures. ...
PloS one
2016, 11(5), e0156199. http://dx.doi.org/10.1371/journal.pone.0156199
Dimerization and Transactivation Domains as Candidates for Functional Modulation and Diversity of Sox9
Geraldo, M. T., Valente, G. T., Nakajima, R. T., Martins, C.
Integrative Genomics Laboratory, Department of Morphology, Institute of Biosciences, Sao Paulo State University–UNESP, Botucatu, SP, 18618–000, Brazil
Systems Biology and Genomics Laboratory, Department of Bioprocess and Biotechnology, Agronomical Science Faculty, Sao Paulo State University–UNESP, Botucatu, SP, 18610–307, Brazil
... Elmer). Finally, a prediction of introns, exons and amino acid sequences were performed
using the online program Softberry FGENESH (http://www.softberry.com/). Phylogenetic
analyses: HMG box, SoxE and Sox9. Three phylogenetic ...
Journal of Plant Biochemistry and Biotechnology
2016, 1-9. DOI: 10.1007/s13562-016-0362-x
Candidate gene prediction and expression profiling of near isogenic lines (NILs) carrying stay-green QTLs in rabi sorghum
Chaudhari, G. N., Fakrudin, B.
1. Institute of Agri-Biotechnology, University of Agricultural Sciences, Dharwad, 580005, India
2. Department of Biotechnology and Crop Improvement, UHS Campus, GKVK Post, Bengaluru, 560 065, India
... The retrieved QTL regions were surveyed for the presence of putative candidate genes using
algorithms such as FGENESH (http://?linux1.?softberry.?com), GENSCAN (http://?genes.?mit.?
edu/?GENSCAN.?html) and GENMARK (http://?exn.?gatech.?edu/?eukhmm.?cgi ...
Angewandte Chemie
2016, 128(2), 674-678. DOI: 10.1002/ange.201509345
Production of New Cladosporin Analogues by Reconstitution of the Polyketide Synthases Responsible for the Biosynthesis of this Antimalarial Agent
Cochrane, R. V. et al.,
Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 (Canada)
Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
... Spliced gene sequences contained within this gene cluster were identified using the hidden
Markov model (HMM) based software FGENESH (Softberry),23 and the resulting intron-less
sequences were analyzed individually by BLAST (NCBI; Figure 1). Figure 1. Figure 1. ...
Journal of plant research
2016, 129(3), 499-512. DOI: 10.1007/s10265-016-0797-0
Characterization of triterpenoid profiles and triterpene synthase expression in the leaves of eight Vitis vinifera cultivars grown in the Upper Rhine Valley
Pensec, F. et al.,
1. Laboratoire Vigne Biotechnologies et Environnement EA 3391, Universite de Haute Alsace, 33 rue de Herrlisheim, 68000, Colmar, France
2. Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, ul. Miecznikowa 1, 02-096, Warsaw, Poland
... The gene named VvTTPS3 was first characterized as two different genes (GSVIVT01029481001
and GSVIVT01029482001), but the study of these sequences using the FGENESH function of
Softberry (http://linux1.softberry.com/berry.phtml) indi- cated that the two sequences ...
Theoretical and Applied Genetics
2016, 1-9. DOI: 10.1007/s00122-016-2722-2
Fine mapping of the dialytic gene that controls multicellular trichome formation and stamen development in tomato
Chang, J. et al.,
1. Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, People’s Republic of China
... 1987; Lincoln et al. 1992). Gene prediction The predicted genes in the target region were
downloaded from SGN (ftp://sgn.cornell.edu). These genes were further analyzed with FGENESH
(http://linux1.softberry.com/) and GENESCAN (http://genes.mit.edu/). ...
Journal of experimental botany
2016, erw187. doi: 10.1093/jxb/erw187
WAX INDUCER1 (HvWIN1) transcription factor regulates free fatty acid biosynthetic genes to reinforce cuticle to resist Fusarium head blight in barley spikelets
Kumar, A. et al.,
1 Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, QC H9X3V9, Canada
2 Centre de Recherche sur les Grains Inc., 740, chemin Trudeau, Saint-Mathieu-de-Beloeil, QC J3G0E2, Canada
... The contigs were downloaded and genes were predicted using the SoftBerry FGENESH program
(http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind). RNA
extraction, cDNA synthesis and quantitative real-time PCR analysis. ...
Chromosoma
2016, 1-11 DOI 10.1007/s00412-016-0601-x
The repetitive DNA element BncDNA, enriched in the B chromosome of the cichlid fish Astatotilapia latifasciata, transcribes a potentially noncoding RNA
Ramos E. et al.,
1. Department of Morphology, Institute of Biosciences, Sao Paulo State University, 18618-689, Botucatu, SP, Brazil
2. Allied Health Sciences Department and Institute for Systems Genomics, University of Connecticut, 06269, Storrs, CT, USA
... janelia.org; Finn et al. 2011), pfam (www.pfam.xfam.org; Finn et al. 2014) and UniProt
(http://www.uniprot.org/blast/; The UniProt Consortium 2015); in addition, gene predictions were
performed using FGENESH at softberry (http://www. softberry.com; Solovyev et al. 2006). ...
Euphytica
2016, Volume 209, Issue 3, pp 725-737 DOI 10.1007/s10681-016-1666-6
Identification and validation of novel alleles of rice blast resistant gene Pi54, and analysis of their nucleotide diversity in landraces and wild Oryza species
Ramkumar, G. et al.,
Crop Improvement Section, Indian Institute of Rice Research
... default settings. Gene structure (length of open reading frame (ORF) and number
of exons/introns, etc. and protein sequences were derived using online tool,
softberry-FGENESH (http://?linux1.?softberry.?com). Numbers of ...
Theoretical and Applied Genetics
2016, 1-16. DOI 10.1007/s00122-016-2723-1
Fine mapping and identification of candidate genes for the sy-2 locus in a temperature-sensitive chili pepper (Capsicum chinense)
Liu, L. et al.,
1. Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, Korea
2. Department of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
... Gene coding regions of the tomato scaffold were predicted by FGENESH+ (http://linux1.softberry.
com). ... repeatmasker.org) and JDotter (http://athena.bioc.uvic.ca). The gene coding regions were
predicted with FGENESH (http://linux1.softberry.com) and BLASTX (https://blast. ...
Ecotoxicology and environmental safety
2016, 124, 363-368. doi:10.1016/j.ecoenv.2015.11.008
Functional and transcript analysis of a novel metal transporter gene EpNramp from a dark septate endophyte (Exophiala pisciphila)
Wei, Y. F. et al.,
a Key Laboratory of Conservation and Utilization for Bioresources and Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, 650091 Yunnan, PR China
b Kunming Police Dog Base of the Ministry of Public Security, Kunming, 650204 Yunnan, PR China
... different fungi. ORF was also predicted using both ORF Finder (http://www.ncbi.nlm.
nih.gov/gorf/orfig.cgi) and SoftBerry-FGENESH (http://linux1.softberry.com/berry.phtml?
topic=fgenesh&group=programs&;subgroup=gfind). Then ...
Fish & shellfish immunology
2016, 49, 154-162. doi:10.1016/j.fsi.2015.12.009
Genome-wide identification of Hsp70 genes in channel catfish and their regulated expression after bacterial infection
Song, L. et al.,
a Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
b Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA
... database using TBLASTN program. The retrieved genome scaffolds were then
predicted by FGENESH in SoftBerry (http://linux1.softberry.com/berry.phtml?topic=
fgenesh&group=programs&subgroup=gfind). The amino acid ...
PloS one
2016, 11(2), e0148422. http://dx.doi.org/10.1371/journal.pone.0148422
A new glabrous gene (csgl3) identified in trichome development in cucumber (Cucumis sativus L.).
Cui, J. Y. et al.,
Institute
... The FGENESH program (Softberry, Inc., Mount Kisco, NY, USA) was used on the 19.6 kb genomic DNA region in scafflold000002 of the 9930 draft genome delimited by dCAPs-19 and dCAPs-21....
... Candidate genes prediction. Potential candidate genes in the target genomic region
were identified using Softberry (http://linux1.softberry.com/all.htm) and the Cucumber
Genome Database (http://www.icugi.org/cgi-bin/ICuGI/index.cgi). ...
Applied biochemistry and biotechnology
2016, 1-28. DOI 10.1007/s12010-016-2114-8
The WRKY Transcription Factor Family in Citrus: Valuable and Useful Candidate Genes for Citrus Breeding
Ayadi, M. et al.,
1. Laboratory of Extremophile Plants. Center of Biotechnology of Borj-Cedria (CBBC), BP 901, Hammam-lif, 2050, Tunisia
2. Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Road, P.O. Box 1177, 3018, Sfax, Tunisia
... net/clementine). All gene structures (exon-intron organization) were predicted by
FGENESH Softberry (http://linux1.softberry.com/berry.phtml) [36]. Multiple Sequence
Alignment, Structural and Phylogenetic Analysis To gain ...
Fish & shellfish immunology
2016, 49, 110-121. doi:10.1016/j.fsi.2015.12.022
Septin genes in channel catfish (Ictalurus punctatus) and their involvement in disease defense responses
Fu, Q. et al.,
a State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
b The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
... with a cutoff E-value of 1e ?10 . Fgenesh program of Molquest software (Softberry
Int.) was used to predict the genes from retrieved genomic scaffold sequences [56].
The simple modular architecture research tool (SMART http ...
Acta Physiologiae Plantarum
2016, 38(6), 1-14. DOI 10.1007/s11738-016-2152-4
The plasma membrane proton pump gene family in cucumber
Wdowikowska, A., Klobus, G.
1. Department of Plant Molecular Physiology, Institute of Experimental Biology, Wroclaw University, Kanonia 6/8, 50-328, Wroclaw, Poland
... sequences of new genes, promoter sequences and 5? untranslated region (5? UTR) as well
as encoded amino acid sequences were predicted and analyzed using the FGENESH program
(hidden Markov model (HMM)-based gene prediction program; softberry.com) with ...
Journal of General Plant Pathology
2016, 82(3), 121-131. DOI 10.1007/s10327-016-0656-9
The global regulator LaeA controls biosynthesis of host-specific toxins, pathogenicity and development of Alternaria alternata pathotypes
Takao, K. et al.,
1. The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8553, Japan
2. Faculty of Agriculture, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8553, Japan
... 2004) as a query. Softberry FGENESH (http://?linux1.?softberry.?com/?berry.?
phtml) was then used to predict the amino acid sequence of the LaeA homolog in
the tomato pathotype of A. alternata. The conserved domain of ...
Journal of General Plant Pathology
2016, Volume 82, Issue 2 , pp 82-88 DOI 10.1007/s10327-016-0647-x
Functional characterization of putative G protein-coupled receptors in the tomato pathotype of Alternaria alternata
Takao, K., Akagi, Y., Tsuge, T., Kodama, M.
1. The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8553, Japan
2. Faculty of Agriculture, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8553, Japan
... al. 2006; Xue et al. 2008) as queries. Softberry FGENESH (http://?linux1.?softberry.?
com/?berry.?phtml) was then used to predict the amino acid sequences of the GPCR
homologs in the A. alternata tomato pathotype. The ...
Molecular medicine reports
2015, 11(4), 3069-3077 DOI: 10.3892/mmr.2014.3054
DHA-1 plasmid-mediated AmpC b-lactamase expression and regulation of Klebsiella pnuemoniae isolates
Luan, Y. et al.,
Department of Medicine Laboratory, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China, Medicine Laboratory, Department of Urology Surgery, Daqing Oilfield General Hospital, Daqing, Heilongjiang 163001, P.R. China
... form pT-AmpD, whose sequence was also detected. The site of the AmpD gene
promoter was predicted by Softberry Fgenesh (http://www.softberry.com) for sequence
analysis. The AmpDP PCR procedure was performed with ...
FEBS letters doi: 10.1016/j.febslet.2015.01.020
2015, 589(5), 598-607.
An evolutionarily-unique heterodimeric voltage-gated cation channel found in aphids
Amey, J. S. et al.,
aDepartment of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
bInstitute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
cSchool of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, United Kingdom
... Gene predictions were facilitated using FGENESH software (www.softberry.com).... Genome organization. FGENESH (Softberry) gene predictions of the coding regions ...
BioMed research international
Volume 2015 (2015), Article ID 149504, 7 pages http://dx.doi.org/10.1155/2015/149504
Molecular characterization of a new alkaline-tolerant xylanase from Humicola insolens Y1
Shi, P. et al.,
1Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
2College of Biological Science and Engineering, Bei Fang University of Nationalities, Yinchuan 750021, China
... 2.4. Sequence Analysis. Vector NTI 10.0 was used for DNA assembly and sequence
analysis. Introns, exons, and transcription initiation sites were predicted using the online
software FGENESH (http://linux1.softberry.com/berry.phtml). ...
Molecular biology reports
2015, 42(2), 535-552. DOI: 10.1007/s11033-014-3797-y
Genome wide in silico characterization of Dof gene families of pigeonpea (Cajanus cajan (L) Millsp.)
Malviya, N. et al.,
Department of BiotechnologyD.D.U. Gorakhpur University Centre for Bioinformatics, School of BiotechnologyBanaras Hindu University
... As for the incorrectly-predicted genes, manual re-annotation was performed using the
on-line web server GENSCAN (http://?genes.?mit.?edu/?GENSCAN.?html) [56] and
FGENESH (http://?linux1.?softberry.?com/?berry.?phtml) [57]. ...
ChemBioChem
2015, 16(17), 2479-2483. DOI: 10.1002/cbic.201500428
Comparison of 10, 11?Dehydrocurvularin Polyketide Synthases from Alternaria cinerariae and Aspergillus terreus Highlights Key Structural Motifs
Cochrane, R. V. et al.,
Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada Department of Chemical and Biomolecular Engineering and, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
... Hidden Markov model (HMM)-based gene sequences contained within this gene
cluster were predicted with FGENESH (Softberry),[34] and the resulting gene
sequences were analyzed individually by using BLAST (NCBI). ...
Applied biochemistry and biotechnology
2015, 175(4), 1960-1970. DOI: 10.1007/s12010-014-1416-y
A new GH43 ?-arabinofuranosidase from Humicola insolens Y1: biochemical characterization and synergistic action with a xylanase on xylan degradation
Yang, X. et al.,
Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research InstituteChinese Academy of Agricultural Sciences
... The sequence assembly and similarity analysis were performed using the Vector NTI Advance
10.0 software (Invitrogen). The online software FGENESH (http://?linux1.?softberry.?com/?berry.?
phtml) was used to predict the transcription initiation sites, introns and exons. ...
Food chemistry
2015, 173, 283-289. http://dx.doi.org/10.1016/j.foodchem.2014.10.022
A thermophilic b-mannanase from Neosartorya fischeri P1 with broad pH stability and significant hydrolysis ability of various mannan polymers
Yang, H. et al.,
Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
... The sequence assembly was performed using the Vector NTI Advance 10.0 software
(Invitrogen). Genes, introns, exons and transcription initiation sites were predicted using
the online software FGENESH (http://linux1.softberry.com/berry.phtml). ...
Fungal biology
2015, 119(7), 551-559. http://dx.doi.org/10.1016/j.funbio.2015.02.007
Expression profiling and functional analyses of BghPTR2, a peptide transporter from Blumeria graminis f. sp. hordei
Droce, A. et al.,
a Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg O, Denmark
b Novo Nordisk A/S, Brennum Park, 3400 Hillerod, Denmark
... 1997) and the BluGen database 'http://www.blugen.org' of the Bgh sequencing project (
Spanu et al. 2010). On the basis of this data a gene model for BghPTR2 was constructed
using FGENESH (SoftBerry) combined with cDNA sequence data. ...
Journal of experimental botany
2015, 66(5), 1271-1290. doi: 10.1093/jxb/eru478
Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea
Bajaj, D. et al.,
1 National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
2 Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
... The structural annotations for different coding and non-coding URR sequence components of
these transcripts were performed using the NCBI ORF Finder (http://www.ncbi.nlm.nih.gov/projects/
gorf), FGNESH (www.softberry.com), ORF Finder (http://bioinformatics.org/sms ...
Biotechnology and Bioengineering
2015 DOI 10.1002/bit.25864
Engineering Rhodosporidium toruloides for increased lipid production
Zhang et al.,
1: Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
2: Department of Bioengineering, University of California, Berkeley, California, United States of America.
... Genome annotation was performed using an automated software pipeline FGENESH++
(http://www.softberry.com) version 3.1.1. Genes were first predicted ab initio using FGENESH... Gene prediction
parameters were obtained from Softberry and were based on Puccinia spp. ...
Insect biochemistry and molecular biology
2015, 65, 1-9. doi:10.1016/j.ibmb.2015.07.009
Alternatively spliced orcokinin isoforms and their functions in Tribolium castaneum
Jiang, H., Kim, H. G., Park, Y
a Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 40071, People's Republic of China
b Department of Entomology, Kansas State University, Manhattan, KS 66506, United States
... Kim et al., 2010). A manual OK-A prediction was performed in the region near
TC005944 and was assisted by the FGENESH program ( Solovyev et al., 2006) from
the Softberry website (http://www.softberry.com). To confirm the ...
Journal of applied genetics
2015, 1-12. DOI: 10.1007/s13353-015-0271-z
Structural characteristics of ScBx genes controlling the biosynthesis of hydroxamic acids in rye (Secale cereale L.)
Bakera et al.,
1. Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, 159 Nowoursynowska Str, 02-776, Warsaw, Poland
2. Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzikow, 05-870, Blonie, Poland
... Bioinformatic analyses were performed by means of the pro- grams listed below using default
settings except for SoftBerry/ FGENESH when monocot plant specific gene-finding param- eters
and Blastn when the selection of nucleotide collection (in Bother databases^ section ...
Physiology and Molecular Biology of Plants
2015, 21(2), 301-304. DOI: 10.1007/s12298-015-0284-
Nucleotide variation and identification of novel blast resistance alleles of Pib by allele mining strategy
Ramkumar, G., Madhav, M. S., Devi, S. R., Prasad, M. S., Babu, V. R
1. Crop Improvement Section, Directorate of Rice Research, Rajendranagar, Hyderabad, 500030, India
... In that analysis, standard error was calculated by bootstrap value with 1000 replicates. Phylogenic
tree was constructed with MEGA - Neighbor- Joining (NJ) method. Gene structure was annotated
using on- line tool softberry- FGENESH (http://linux1.softberry.com). ...
IUBMB Life
2015, Volume 68, Issue 2, pages 122–135, February 2016 DOI: 10.1002/iub.1464
Identification of differentially expressed three novel transcript variants of mouse ARNT gene
Ishqi, H. M., Ur Rehman, S., Sarwar, T., Husain, M. A., Tabish, M.
Institute
... finding tools. Gene finding tools used in our study were HMM gene (http://www.cbs.
dtu.dk/services/HMMgene/), Genebuilder (http://www.itba.mi.cnr.it/webgene/) and
FGENESH (http://linux1.softberry.com/berry.phtml). "Fex" available ...
Journal of basic microbiology
2015, 55(5), 591-600. DOI: 10.1002/jobm.201300814
Thc6 protein, isolated from Trichoderma harzianum, can induce maize defense response against Curvularia lunata
Fan, L et al.,
Department of Resource and Environmental Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
... After predicting online on the softberry website (http://linux1.softberry.com/berry.phtml?
topic=fgenesh&group=programs&subgroup=gfind) and using PCR for confirmation, we
cloned a 710 bp cDNA fragment containing the T-DNA insertion site. ...
Theoretical and Applied Genetics
2015, 128(10), 2099-2111. DOI: 10.1007/s00122-015-2570-5
Fine mapping of powdery mildew resistance genes PmTb7A. 1 and PmTb7A. 2 in Triticum boeoticum (Boiss.) using the shotgun sequence assembly of chromosome 7AL
Chhuneja, P et al.,
1. School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141 004, India
2. Institute of Plant Biology, University of Zurich, Zurich, Switzerland
... softberry.com/berry.phtml?topic=fgenesh&group=progra ms&subgroup=gfind). ... The Prot_Map
(http://linux1.soft- berry.com/berry.phtml?topic=prot_map&group=program s&subgroup=xmap)
was used to align protein sequences with their corresponding nucleotide sequences. ...
Biotechnology letters
2015, 37(4), 907-919 DOI: 10.1007/s10529-014-1733-9
GhDRIN1, a novel drought-induced gene of upland cotton (Gossypium hirsutum L.) confers abiotic and biotic stress tolerance in transgenic tobacco
Dhandapani, G. et al.,
1. National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
2. Department of Plant Science, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
... Invitrogen). The ORF was identified by the FGENESH analysis using softberry software
(www.?softberry.?com). ... sequenced. The ORF of the gene was identified by FGENESH
of softberry online software using aligned sequence. ...
Plant Science
2015, Volume 234, May 2015, Pages 50–59, doi:10.1016/j.plantsci.2015.02.005
Modification of plasma membrane NADPH oxidase activity in cucumber seedling roots in response to cadmium stress
Jakubowska, D., Janicka-Russak, M., Kabala, K., Migocka, M., Reda, M.
Department of Plant Molecular Physiology, Institute of Experimental Biology, University of Wroclaw, Kanonia Street 6/8, 50-328 Wroclaw, Poland
... homologs of genes encoding NADPH oxidase. Identified sequences were then
analyzed using FGENESH and FGENESH+ tools (Softberry, Inc., Mount Kisco, New
York; www.softberry.com). ClustalW was used to perform the ...
Molecular Genetics and Genomics
2015, 290(2), 443-460. DOI: 10.1007/s00438-014-0927-0
Molecular evolution and functional divergence of X-intrinsic protein genes in plants
Venkatesh, J., Yu, J. W., Gaston, D., Park, S. W.
1. Department of Molecular Biotechnology, Konkuk University, 1, Hwayang-dong, Gwangjin-gu, Seoul, Republic of Korea
2. Department of Pathology, Dalhousie University, Halifax, NS, Canada
... GmXIP1;1, GmXIP1;3, LuXIP2;2, RcXIP1;1, RcXIP2;1, RcXIP2;2 and SlXIP1;6), gene
structures were predicted using FGENESH softberry tool (http://linux1.softberry.
com/berry.phtml) due to uncertainty in the original gene models. ...
Marine genomics
Volume 24, Part 2, December 2015, Pages 147–157 doi:10.1016/j.margen.2015.03.010
Discovery of germline-related genes in Cephalochordate amphioxus: A genome wide survey using genome annotation and transcriptome data
Yue, J. X., Li, K. L., Yu, J. K.
a Ecology and Evolutionary Biology, Department of BioSciences, Rice University, 6100 Main Street, Houston, TX 77005, USA
b Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
... We carried out the re-annotation using Softberry's FGENESH program (http://www.
softberry.com/berry.phtml?topic=fgenesh) ( Salamov and Solovyev, 2000) with B.
floridae specific gene discovery parameters provided by Softberry. ...
Journal of Applied Microbiology
2015 DOI: 10.1111/jam.13036
Occidiofungin is an Important Component Responsible for the Antifungal Activity of Burkholderia pyrrocinia Strain Lyc2
Wang, X. Q. et al.,
Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong, China
Collaborative Innovation Centre for Annually High Yield and High Efficiency Production of Wheat and Corn, Shandong Agricultural University, Tai'an, Shandong, China
... Biosciences, Carlsbad, CA) and Geneious R8 (Biomatters Ltd.). Open reading frames (ORFs)
and genes were predicted by the Softberry FGENESH program (Salamov and Solovyev ... prediction
was accomplished using the web-based software BRROM in the Softberry Page 9. ...
Applied biochemistry and biotechnology
2015, 177(1), 207-216. DOI: 10.1007/s12010-015-1738-4
Expression of Finger Millet EcDehydrin7 in Transgenic Tobacco Confers Tolerance to Drought Stress
Singh et al.,
1. National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
2. Institute of Biotechnology, Acharya N.G. Ranga Agricultural University, Hyderabad, 500030, India
... USA). Full-length ORF was obtained with the help of gene finding online tool FGENESH
(softberry.?com). ... sequenced. The coding region of the gene was identified by FGENESH
of softberry online software using aligned sequence. ...
Molecular biology reports
2015, 42(7), 1163-1174. doi:10.?1007/?s11033-015-3853-2
Genome-wide identification and expression profiling of the late embryogenesis abundant genes in potato with emphasis on dehydrins
Charfeddine, S., Saidi, M. N., Charfeddine, M., & Gargouri-Bouzid, R.
Unite Enzymes et Bioconversion, Ecole Nationale d’Ingenieurs de Sfax; Centre de Biotechnologie de Sfax
.. Proteins without any appropriate motif were re-predicted and corrected using Fgenesh
software (http://?linux1.?softberry.?com/?berry.?phtml) using dicotyledon plant
models. Proteins with no reliable prediction were removed. ...
Molecular medicine reports
2015, 11(4), 3069-3077. DOI: 10.3892/mmr.2014.3054
DHA-1 plasmid-mediated AmpC ?-lactamase expression and regulation of Klebsiella pnuemoniae isolates
Luan, Y. et al.,
Department of Medicine Laboratory, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China, Medicine Laboratory, Department of Urology Surgery, Daqing Oilfield General Hospital, Daqing, Heilongjiang 163001, P.R. China
... form pT-AmpD, whose sequence was also detected. The site of the AmpD gene
promoter was predicted by Softberry Fgenesh (http://www.softberry.com) for sequence
analysis. The AmpDP PCR procedure was performed with ...
Gene
2015, 556(2), 106-112. doi:10.1016/j.gene.2014.11.035
Molecular cloning, characterisation and mRNA expression of the ryanodine receptor from the peach-potato aphid, Myzus persicae
Troczka, B. J. et al.,
a Biological Chemistry and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
b Institute of Molecular & Experimental Medicine, Cardiff University School of Medicine, Wales Heart Research Institute, Heath Park, Cardiff CF14 4XN, UK
... The intron/exon boundaries were determined using Spidey (http://www.ncbi.nlm.nih.gov/spidey/)
and Softberry FGENESH (http://linux1.softberry.com/all.htm) software and by manual sequence
analysis using Geneious v5.5 (Biomatters Ltd). 3. Results and discussion. 3.1. ...
Transgenic research
2015, 24(5), 847-858. DOI: 10.1007/s11248-015-9878-4
Identification of candidate MLO powdery mildew susceptibility genes in cultivated Solanaceae and functional characterization of tobacco NtMLO1
Appiano, M. et al.,
1. Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
2. Department of Plant, Soil and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
... The number of transmembrane domains was predicted using the online software TMHMM
(http://?www.?cbs.?dtu.?dk/?services/?TMHMM/?). The putative number of introns was obtained
using the online service FGENESH of Softberry (http://?www.?softberry.?com/?). ...
Annals of Forest Science
2015, 72(8), 1043-1052. DOI: 10.1007/s13595-015-0502-9
Molecular marker associated with a deleterious recessive anomaly in Eucalyptus grandis seedlings
Fuchs, M. C. et al.,
1. Departamento de Genetica, Instituto de Biociencias, Universidade Estadual Paulista (UNESP), Distrito de Rubiao Jr s/n, Botucatu, SP, 18618-970, Brazil
2. Departamento de Biologia, Campus Sorocaba, Universidade Federal de Sao Carlos (UFSCar), Rod. Joao Leme dos Santos, Km 110, Sorocaba, SP, 18052-780, Brazil
... 1997 ). The identified ESTs with high identity were translated by ExPASy translate
tool (http://?expasy.?org) (Gasteiger et al. 2003 ) and analyzed using FGENESH
(Softberry, http://?www.?softberry.?com) to predict the protein. ...
Current Biotica
2015, 8(4), 351-358.
A comprehensive computational analysis of cis-regulatory elements for anthocyanin biosynthesis genes in tomato (Solanum lycopersicum L.)
Dinabandhu, A.
ICAR- National Research Center on Plant Biotechnology, Pusa Campus, New Delhi-110012
... of International Tomato Annotation Group release 2.4 version was used from http://solgenomics.
net/ and anthocyanin genes were predicted by using BLAST- Basic Local Alignment Search Tool
(http://blast.ncbi.nlm.nih.gov/ Blast.cgi) and FGENESH (www.softberry.com) gene ...
International Biodeterioration & Biodegradation, 93, 186-194.
2014, 93, 186-194. DOI: 10.1016/j.ibiod.2014.06.001
Purification and characterization of a thermotolerant laccase isoform in Trametes trogii strain and its potential in dye decolorization
Yan J. et al.,
a Biotechnology Research Center of Life Science and Technology College, Kunming University of Science and Technology, Kunming Yunnan 650500, PR China
b College of Life Science, the Southwest Forest University, Kunming Yunnan 650224, PR China
... The gene structure and amino acid sequences of full laccase were predicted and analyzed
with Soft Berry-FGENSH/HMM-based gene structure prediction (http://linux1.softberry.com/
berry.phtml?topic=fgenesh&group=programs&subgroup=gfind). ...
Tree Genetics & Genomes
2014, 10(2), 251-260. DOI: 10.1007/s11295-013-0678-9
Cloning and functional characterization of the Rvi15 (Vr2) gene for apple scab resistance
Schouten H. J. et al.,
1. Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
2. Inova Fruit, P.O. Box 222, 4190 CE, Geldermalsen, The Netherlands
... 2010b) was copied from the NCBI database (accession number GU295057.1). The
Vr2-A, Vr2-B, and Vr2-C amino acid sequences in GMAL 2473 were predicted by means
of the publicly available software FGENESH from SoftBerry. ...
PloS one
2014, 9(4), e93560. DOI: 10.1371/journal.pone.0093560
Whole Genome and Global Gene Expression Analyses of the Model Mushroom Flammulina velutipes Reveal a High Capacity for Lignocellulose Degradation
Park Y. J. et al.,
Department of Biomedical Chemistry, Konkuk University, Chung-Ju, Republic of Korea; Macrogen Inc., Seoul, Republic of Korea
... Gene identification was carried out using several methods, including ab initio gene structure
prediction (Fgenesh; http://www.softberry.com), a homology-based approach (Fgenesh+;
http://www.softberry.com), and transcriptome-based gene identification (Cufflinks; http://cufflinks ..
Cellular signalling
2014, 26(6), 1155-1165. DOI: 10.1016/j.cellsig.2014.02.003
Mature miR-183, negatively regulated by transcription factor GATA3, promotes 3T3-L1 adipogenesis through
inhibition of the canonical Wnt/b -catenin signaling pathway by targeting LRP6
Chen C. et al.,
a Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
... BDGP (http://www.fruitfly.org/seq_tools/promoter.html) and SoftBerry (http://linux1.softberry.com/
berry.phtml?topic=fgenesh&group=programs&subgroup=gfind) computer programs were utilized
to analyze miR-183 gene structure, including TSS, CDS, and polyA signal. ...
Euphytica
2014, 196(3), 341-348. DOI: 10.1007/s10681-013-1037-5
Fine mapping of the uniform immature fruit color gene u in cucumber (Cucumis sativus L.)
Yang X et al.,
1. School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Minhang District, Shanghai, 200240, China
2. Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, 201602, China
... (Voorrips 2002 ). Gene prediction in the target genomic DNA regions was performed
using the program FGENESH (Salamov and Solovyev 2000 ) (http://?linux1.?softberry.?
com/?), and the results were checked manually. Results. ...
Molecular Breeding
2014, 1-13. DOI: 10.1007/s11032-014-0088-1
Fine genetic mapping of a locus controlling short internode length in melon (Cucumis melo L.)
Hwang J. et al.,
1. Department of Horticultural Bioscience, Pusan National University, Miryang, 627-706, Republic of Korea
2. Gyeongnam Agricultural Research and Extension Services, Jinju, 663-985, Republic of Korea
... market type cucumber inbred line “9930” (Li et al. 2011b ) were determined using
FGENESH software (Softberry Inc., Mount Kisco NY, USA; http://?sunl.?softberry.?
com/?). Primer pairs were designed to amplify these exon ...
Fungal biology
2014, 118(2), 228-241. DOI: 10.1016/j.funbio.2013.12.001
The Podosphaera fusca TUB2 gene, a molecular “Swiss Army knife” with multiple applications in powdery mildew research
Vela-Corcia, D., Bellon-Gomez, D., Lopez-Ruiz, F., Tores, J. A., & Perez-Garcia, A.
a Instituto de Hortofruticultura Subtropical y Mediterranea “La Mayora” - Universidad de Malaga - Consejo Superior de Investigaciones Cientificas (IHSM-UMA-CSIC), Departamento de Microbiologia, Universidad de Malaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Malaga, Spain
b Instituto de Hortofruticultura Subtropical y Mediterranea “La Mayora” - Universidad de Malaga - Consejo Superior de Investigaciones Cientificas (IHSM-UMA-CSIC), Estacion Experimental “La Mayora”, 29750 Algarrobo-Costa, Malaga, Spain
... Potential open reading frames (ORFs), introns, and exons were predicted using
FGENESH software from SoftBerry (http://linux1.softberry.com/berry.phtml). Amino acid
alignments were performed with the CLC Main Workbench (Aarhus). ...
Gene
2014, 534(2), 204-217. DOI: 10.1016/j.gene.2013.10.058
Genomic organization, sequence characterization and expression analysis of Tenebrio molitor apolipophorin-III in response to an intracellular pathogen, Listeria monocytogenes
Noh J. Y. et al.,
a Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
b Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan City 336-745 Republic of Korea
... sequencing method (see above). The fosmid library sequence information was used
for predicting TmapoLp-III gene architecture using FGENESH 2.6 software from Softberry
(http://linux1.softberry.com/berry.phtml/). The sequence of ...
Developmental & Comparative Immunology
2014, 46(2), 208-221. DOI: 10.1016/j.dci.2014.04.009
Gene structure, cDNA characterization and RNAi-based functional analysis of a myeloid differentiation factor 88 homolog in Tenebrio molitor larvae exposed to Staphylococcus aureus infection
Patnaik B. B. et al.,
a Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
b Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan City 336-745, Republic of Korea
... sequencing method (see above). 2.4. Sequence analysis. The fosmid clone
corresponding to TmMyD88 was analyzed using the FGENESH 2.6 program at
Softberry (http://linux1.softberry.com/berry.phtml/). The 5?-flanking ...
The ScientificWorld Journal
Volume 2014, Article ID 619746, 7 pages DOI: /10.1155/2014/619746
Genetic diversity analysis of Hypsizygus marmoreus with target region amplification polymorphism.
Qiu, C., Yan, W., Deng, W., Song, B., Li, T.
1 Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of
Applied Microbiology, State Key Laboratory of Applied Microbiology South China, Guangdong Institute of Microbiology,
Guangzhou 510070, China
2Department of Biology, Chengdu Normal University, Chengdu 611130, China
... introns of sequence analyses were predicted by web-based program FGENESH [37-39]
(http://linux1.softberry.com/berry.phtml) Page 6. ... function proteins based on BLAST prediction
and open reading frame (ORF) analysis by web-based SoftBerry (Supplementary files 2). ...
Gene
Volume 546, Issue 2, 10 August 2014, Pages 250–256 DOI: 10.1016/j.gene.2014.06.001
Nucleotide diversity of Pita, a major blast resistance gene and identification of its minimal promoter.
Ramkumar G. et al.,
a Biotechnology, Crop Improvement, DRR-ICAR, Hyderabad-30, India
b Plant Pathology, DRR-ICAR, Hyderabad-30, India
... other default settings. Gene structure (length of open reading frame (ORF), number
of exons/introns, etc.) and protein sequences were predicted using online tool
softberry — FGENESH (http://linux1.softberry.com). Number of ...
Fungal biology
2014, 118(5), 453-461. DOI: 10.1016/j.funbio.2014.03.003
Molecular cloning and functional analysis of a H< sup>+-dependent phosphate transporter gene from the ectomycorrhizal fungus Boletus edulis in southwest China
Wang J. et al.,
Laboratory of Conservation and Utilization for Bioresources, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, Yunnan Province, PR China
... Bioinformatic analysis. The open reading frame (ORF) was predicted using the ORF Finder
(http://www.ncbi.nlm.nih.gov/gorf/orfig.cgi) and the SoftBerry-FGENESH database
(http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind). ...
Crop Science
2014, 54(3), 873-881. DOI: 10.2135/cropsci2013.09.0598
Fine Mapping of the Maize Cross-Incompatibility Locus Gametophytic Factor 1 (ga1) Using a Homogeneous Population.
Liu, X et al.,
2. Ajinomoto-Genetika Research Institute, 1st Dorozhny Pr. 1-1, 117545, Moscow, Russia
1. Syngas Biofuels Energy, Inc., P.O. Box 300819, Houston, TX, 77230, USA
... The maize gene set (www.maizesequence.org) and website-based software FGENSH
(www.softberry.com) was applied to predict and filter the putative genes from the mapping interval.
RESULTS. The Homogeneous Population Mapping Approach for Ga1-S Allele. ...
Applied microbiology and biotechnology
2014, 98(1), 285-296. DOI: 10.1007/s00253-013-5289-8
MpigE, a gene involved in pigment biosynthesis in Monascus ruber M7
Liu Q et al.,
1. College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People’s Republic of China
3. National Key Laboratory of Agro-Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People’s Republic of China
... Amino acid sequence encoded by MpigE was predicted using SoftBerry's FGENESH
program (http://linux1.softberry. com/berry.phtml), and the MpigE functional regions were
analyzed using the Pfam 27.0 program (http://pfam.sanger.ac. uk/). ...
Gene
2014 DOI: 10.1016/j.gene.2014.01.008
The homoeologous genes encoding chalcone-flavanone isomerase in Triticum aestivum L.: structural characterization and expression in different parts of wheat plant
Shoeva, O. Y., Khlestkina, E. K., Berges, H., & Salina, E. A.
a Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
b Novosibirsk State University, 630090, Russia
c INRA-CNRGV, Toulouse, 31326, France
... Gene annotation was performed by FGENESH program (Softberry Inc.,
linux1.softberry.com/berry.phtml) and confirmed by comparison of genomic nucleotide
sequence with available ESTs. MEGA v5.1 software (Tamura et al. ...
Applied microbiology and biotechnology
2014,Volume 98, Issue 11, pp 4987-4994. DOI: 10.1007/s00253-014-5509-x
A promiscuous prenyltransferase from Aspergillus oryzae catalyses C-prenylations of hydroxynaphthalenes in the presence of different prenyl donors
Pockrandt, D., Sack, C., Kosiol, T., & Li, S. M.
1. Institut fur Pharmazeutische Biologie und Biotechnologie, Philipps-Universitat Marburg, Deutschhausstrasse 17A, 35037, Marburg, Germany
... Computer-assisted sequence analysis The software FGENESH (Softberry, Inc; http://www.
softberry.com/berry.phtml) was used for prediction of exon and intron sequences. Alignments
of amino acid sequences were carried out by using the program BLAST (http://blast. ...
Marine genomics
2014, 13, 1-9. DOI: 10.1016/j.margen.2013.10.004
Presence of two tumor necrosis factor ( tnf)-? homologs on different chromosomes of zebrafish ( Danio rerio) and medaka ( Oryzias latipes)
Kinoshita, S., Biswas, G., Kono, T., Hikima, J., Sakai, M.
a Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
b Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
c Interdisciplinary Research Organization, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
... For medaka tnf-n, the nucleic acid sequence was retrieved from medaka chromosome 16
(25694643-25698981) (Ensembl release 72) and amino acid (aa) sequence, exons and introns
were predicted using FGENESH in SoftBerry (http://linux1.softberry.com/berry.phtml). ...
Physiologia plantarum
, 150(1), 32-45. DOI: 10.1111/ppl.12064
Transcriptional regulation of the V?ATPase subunit c and V?PPase isoforms in Cucumis sativus under heavy metal stress
Kabala K. et al.,
Department of Plant Molecular Physiology, Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland
... cucumber sequences were then analyzed using gene finding programs identifying full-length
cDNA sequences (comprising the 5? and 3? ends): GeneMark (http://exon.biology.gatech.edu/
eukhmm.cgi) and FGENESH as well as FGENESH+ on the SoftBerry server (http ...
Journal of basic microbiology
28 APR 2014 DOI: 10.1002/jobm.201300814
Fan, L., Fu, K., Yu, C., Li, Y., Li, Y., & Chen, J. (2014). Thc6 protein, isolated from Trichoderma harzianum, can induce maize defense response against Curvularia lunata
Fan L. et al.,
Department of Resource and Environmental Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
... After predicting online on the softberry website (http://linux1.softberry.com/berry.phtml?
topic=fgenesh&group=programs&subgroup=gfind) and using PCR for confirmation, we
cloned a 710 bp cDNA fragment containing the T-DNA insertion site. ...
Plant Molecular Biology Reporter
2014, 1-21 DOI: 10.1007/s11105-014-0729-x
A Gene Encoding Cold-Circadian Rhythm-RNA Binding-Like Protein (CCR-Like) from Upland Cotton (Gossypium hirsutum L.) Confers Tolerance to Abiotic Stresses in Transgenic Tobacco
Dhandapani G. et al.,
1. National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
2. Department of Plant Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
... The amplified cDNA was cloned in pGEM T-Easy vector and sequenced. The full- length cDNA
sequence and coding sequence (CDS) were identified by the FGENESH analysis of softberry
software (www.softberry.com/) and the sequence has been submitted to the GenBank. ...
Journal of experimental botany
2014, eru041. DOI: 10.1093/jxb/eru041
Sixteen cytosolic glutamine synthetase genes identified in the Brassica napus L. genome are differentially regulated depending on nitrogen regimes and leaf senescence.
Orsel M. et al.,
1 INRA, UMR 1349 Institut de Genetique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Universite de Rennes 1, F-35653 Le Rheu, France
2 INRA, UMR 1345 Institut de Recherche en Horticulture et Semences, F-49071 Beaucouze, France
...The deduced mRNA sequences (Supplementary Data File S5), obtained using FGENESH software available on the SoftBerry website (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group =programs&subgroup=gfind), showed very a high similarity with the contig sequences (Table 4) and allowed the gene structures to be deduced (Fig. 2). ...
Mycobiology
2014, 42(1), 34-40. DOI:10.5941/MYCO.2014.42.1.34
Three New Non-reducing Polyketide Synthase Genes from the Lichen-Forming Fungus Usnea longissima
Wang, Y., Wang, J., Cheong, Y. H., Hur, J. S.
1 Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry, Kunming 650-204, China.
2 Korean Lichen Research Institute, Sunchon National University, Suncheon 540-742, Korea.
... Ltd. (Seoul, Korea). The potential open reading frame (ORF) was scanned with FGENESH [22]
using Aspergillus as the matrix (http://linux1.softberry.com). The putative function of these ORFs
was determined using a basic local alignment search tool (BLAST). ...
Molecular Breeding
2014, 33(4), 953-959. DOI:10.1007/s11032-013-0009-8
Intron loss in the chalcone-flavanone isomerase gene of rye
Khlestkina E. K., Shoeva O. Y.
1. Institute of Cytology and Genetics SB RAS, Lavrentjeva Ave. 10, 630090, Novosibirsk, Russia
2. Novosibirsk State University, Novosibirsk, Russia
... Gene structure was determined by FGENESH software (http://?linux1.?softberry.?com/?berry.?
phtml, Solovyev 2007 ) and confirmed by comparison of nucleotide sequence with the rye
expressed sequence tag BE705313 (http://?www.?ncbi.?nlm.?nih.?gov/?Database/?). ...
Food chemistry
2014, 148, 381-387 DOI: 10.1016/j.foodchem.2013.10.062
Two xylose-tolerant GH43 bifunctional ?-xylosidase/?-arabinosidases and one GH11 xylanase from Humicola insolens and their synergy in the degradation of xylan
Yang X. et al.,
a Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
b Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
... deduce the amino acid sequences, respectively. The online software FGENESH
(http://linux1.softberry.com/berry.phtml) was used to predict the transcription initiation
sites, introns and exons. SignalP4.0 server (http://www.cbs ...
Acta Biochimica Polonica
2014, 61(1), 19-22. on-line at: www.actabp.p
Conversion of a diversity arrays technology marker differentiating wild and cultivated carrots to a co-dominant cleaved amplified polymorphic site marker
Macko-Podgorni A. et al.,
1 Institute of Plant Biology and Biotechnology, University of Agriculture Krakow, Krakow, Poland;
2 Department of Horticulture, University of
Wisconsin-Madison, Madison, USA;
3 USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin, Madison, USA
... reported by Iorizzo et al. (2012) with blastn on a local BLAST server. The identified
con- tig was searched for presence of coding regions using FGENESH
(http://linux1.softberry.com/berry.phtml). The sequence was searched for ...
Molecular biology reports
July 2014, Volume 41, Issue 7, pp 4305-4312 DOI:10.1007/s11033-014-3301-8
RNAi Mediated curcin precursor gene silencing in Jatropha (Jatropha curcas L.)
Patade V. Y. et al.,
1. Defence Institute of Bio-Energy Research, Haldwani-263 139, Nainital, Uttarakhand, India
... commercially (Eurofins, India). The sequence was analyzed for homology using Blast
program [ 22 ]. The gene structure was predicted using FGENESH 2.6 tool
(http://?linux1.?softberry.?com/?berry.?phtml). The Motif scanning ...
Nature
2014, 511(7508), E7-E9. DOI:10.1038/nature13446
TH2 and Treg candidate genes in elephant shark
Dijkstra, J. M.
Institute for Comprehensive Medical Science, Fujita Health University, Dengaku-gakubo 1-98, 470-1192 Toyoake, Aichi, Japan
... 2, the loop between ?-helices A and B; exon 3, ?-helices B and C; exon 4, ?-helix D. Genes without
messenger RNA reports were predicted from genomic DNA sequences using GENSCAN
(http://genes.mit.edu/GENSCAN.html) or FGENESH (http://linux1.softberry.com/berry ...
Plant Breeding
Volume 133, Issue 4, pages 470–479, August 2014 DOI:10.1111/pbr.12190
Genetic and functional analysis of tocopherol biosynthesis pathway genes from rapeseed (Brassica napus L.)
Fritsche S. et al.,
1 Plant Breeding Institute, Christian-Albrechts University of Kiel, Kiel, Germany
2 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
... Institute 2012). Sequence comparisons were performed with the basic local
alignment search tool (BLAST). Intron–exon structures were predicted with the
bioinformatic tool FGENESH (SoftBerry FGENESH 2007). The NCBI ...
Plant molecular biology
2014, 84(1-2), 95-110 DOI:10.1007/s11103-013-0121-5
Association of jacalin-related lectins with wheat responses to stresses revealed by transcriptional profiling
Song M. et al.,
1. Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People’s Republic of China
2. Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, 270-0061, Baiyun Road, Guiyang, 550008, People’s Republic of China
... overlapped regions. Gene prediction was then performed using the gene-finding
program FGENESH (http://?www.?softberry.?com/?), and the coding DNA sequences
were verified by alignment with the homologous ESTs. Domain ...
DNA Research
2014, dsu016 DOI:10.1093/dnares/dsu016
Evolutionary History of Trihelix Family and Their Functional Diversification
Qin Y. et al.,
1 State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China
2 Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Republic of Korea
... a cut-off value of e ?10 . As for confirmation of the predicted genes, manual correction
was performed using the online web server FGENESH (http://linux1.softberry.com/
berry.phtml). 28 The confirmed sequences were further ...
Gene
2014, 544(1), 83-92 DOI:10.1016/j.gene.2014.04.046
Genome-wide analysis of terpene synthases in soybean: functional characterization of GmTPS3
Liu J. et al.,
a National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
b Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai 201403, China
... soybean genome sequence assembly using TBLASTN. The gene prediction program
FGENESH (http://www.softberry.com) was used to predict the open reading frames
of putative TPS genes. Protein sequences deduced from the ...
Frontiers in Plant Science | Plant Genetics and Genomics
2014, 5, 339. DOI:10.3389/fpls.2014.00339
Annotation and sequence diversity of transposable elements in common bean (Phaseolus vulgaris)
Jackson, S.
1 Center forAppliedGeneticTechnologies,UniversityofGeorgia,Athens,GA,USA
2 US DepartmentofEnergyJointGenomeInstitute,WalnutCreek,CA,USA
... carry an extra ORF coding envelope-like proteins, the internal regions of 65 Ty1-copia and 78
Ty3-gypsy families were annotated using FGENESH (http://linux1.softberry.com) and ...
(http://linux1.softberry.com) and GENSCAN (http://genes.mit.edu/GENSCAN.html) programs. ...
Plant Molecular Biology Reporter
2014, 32(2), 476-486. DOI: 10.1007/s11105-013-0666-0
Molecular Cloning and Characterization of a Novel Polygalacturonase Gene, BcMF24, Involved in Pollen Development of Brassica campestris ssp. chinensis
Yu Y. et al.,
1. Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
... Full CDS sequences were analyzed by FGENESH (http://linux1.softberry.com/berry.phtml?topic=
fgenesh&group=programs&subgroup=gfind), and the molecular characteristic of the deduced
protein was viewed on the ExPASy (http://web.expasy.org/compute_pi/). ...
Middle-East Journal of Scientific Research
2014, 20(3), 391-395. DOI:10.5829/idosi.mejsr.2014.20.03.11465
An Integrated Approach to Functional Genomics: Construction of a Novel Reporter Genomic Library for Osmium baselicum Plant.
Shah, G. C., Gupta, V., Khanuja, S. P. S.
1 Rajiv Gandhi College Satna M.P. India 2 Entral Institute of Medicinal and Aromatic Plant Lucknow U.P. India
... a new family, the oxidatively stable proteases previously p a r a m e t e r s thought to be present
only in bacteria. Phylogenetic http:linux1.softberry.coberry.phtml?topic=fgenesh&grp= studies
showed that many gene duplications and loss ograms&sub group=gfind. ...
Applied microbiology and biotechnology
2014, 98(11), 5019-5028. DOI:10.1007/s00253-014-5533-x
A novel bifunctional pectinase from Penicillium oxalicum SX6 with separate pectin methylesterase and polygalacturonase catalytic domains
Tu T. et al.,
1. Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People’s Republic of China
... as Lu and Moriyama (2004) described. Transcription initiation sites, intron, and exon
were predicted using the online software FGENESH (http://linux1.softberry.
com/berry.phtml/). Nucleotide and deduced amino acid sequence ...
Journal of industrial microbiology & biotechnology
2014, 41 (7), 1071-1083. DOI:10.1007/s10295-014-1453-0
A new acidophilic endo-b-1, 4-xylanase from Penicillium oxalicum: cloning, purification, and insights into the influence of metal ions on xylanase activity
Liao H. et al.,
1. Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
2. Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
... Putative signal peptides were predicted using signalP (http://www.cbs.dtu.dk/services/
signalP/). The exon–intron structure of the full-length gene was predicted using the online
software fgenesh (http://linux1.softberry.com/ berry.phtml). ...
Crop and Pasture Science
2014, 65(1), 38-45. DOI:10.1071/CP13140
Isolation and characterisation of cytosolic glutamine synthetase (GSe) genes and association with grain protein content in durum wheat
Gadaleta, A. et al.,
A Department of Soil, Plant and Food Sciences, Section of Genetics and Plant Breeding, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A – 70126 Bari, Italy.
... Genes prediction was conducted with the FGENESH program (http://linux1.softberry.com/berry.
phtml?topic=fgenes handgroup=programsandsubgroup=gfind). Consensus exon/ introns
boundaries were confirmed using grass expressed sequence tag sequences aligned to the ...
ChemBioChem
2014, 15(1), 108-116. DOI:10.1002/cbic.201300610
AstPT Catalyses both Reverse N1?and Regular C2 Prenylation of a Methylated Bisindolyl Benzoquinone
Tarcz S. et al.,
Philipps-Universitat Marburg, Institut fur Pharmazeutische Biologie und Biotechnologie, Deutschhausstrasse 17A, 35037 Marburg (Germany)
... Computer-assisted sequence analysis: The software packages DNASIS (version 2.1; Hitachi
Software Engineering, San Bruno, CA, USA) and FGENESH (Softberry, Inc; http://www.softberry.
com/berry.phtml) were used for intron prediction and sequence analysis, respectively. ...
Molecular biology reports
2014, 1-12. DOI:10.1007/s11033-014-3360-x
GhPSY, a phytoene synthase gene, is related to the red plant phenotype in upland cotton (Gossypium hirsutum L.)
Cai C. et al.,
1. State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
... Gene prediction was performed using the Fgenesh program in MolQuest software v1.3.1
(http://?linux1.?softberry.?com/?berry.?phtml), and predicted genes and their GO (Gene Ontology)
categories were annotated with the Blast2GO program ([ 18 ], http://?www.?blast2go ...
PloS one
2014, 9(1), e87723. DOI:10.1371/journal.pone.0087723
Citrus sinensis Annotation Project (CAP): A Comprehensive Database for Sweet Orange Genome
Wang, J. et al.,
Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China, School of Science, Huazhong Agricultural University, Wuhan, P.R. China
... 8, detailed information includes the final gene model, RNA-seq and RNA-PET data from different
tissues, ESTs from sweet orange and other citrus species, and four ab initio gene prediction tools,
ie, Genscan [17], GeneID [18], FgeneSH (http://linux1.softberry.com/berry.phtml ...
Genome biology and evolution
2014, evu112 DOI: 10.1093/gbe/evu112
Recurrent horizontal transfers of Chapaev transposons in diverse invertebrate and vertebrate animals
Zhang, H. H., Feschotte, C., Han, M. J., Zhang, Z.
1School of Life Sciences, Chongqing University, Chongqing 400044, China
2 College of Life Sciences, Jiujiang University, Jiujiang 332000, China
... Sequence analysis Potential open reading frame (ORF) of Chapaev elements used in this study
was predicted using FGENESH (http://linux1.softberry.com/berry.phtml), GENSCAN
(http://genes.mit.edu/GENSCAN.html) or getorf in EMBOSS-6.3.1 package (Rice et al. 2000) ...
Molecular Genetics and Genomics
April 2014. DOI:10.1007/s00438-014-0848-y
High-resolution genetic mapping of rice bacterial blight resistance gene Xa23
Wang C. et al.,
1. National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081, People’s Republic of China
2. Liaocheng University, Liaocheng, 252059, Shandong Province, People’s Republic of China
... Based on the targeted region of Xa23 locus, genomic sequence of nipponbare between the
markers lj138 and a83B4 was downloaded from nCBI (http://www.ncb i.nlm.nih.gov) and
analyzed using the online software FGeneSH (http://linux1.softberry.com/). ...
Applied Microbiology and Biotechnology
October 2013 DOI: 10.1007/s00253-013-5289-8
MpigE, a gene involved in pigment biosynthesis in Monascus ruber M7
Liu, et al.,
1. College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People’s Republic of China
3. National Key Laboratory of Agro-Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People’s Republic of China
... Amino acid sequence encoded by MpigE was predicted using SoftBerry's FGENESH
program (http://linux1.softberry. com/berry.phtml), and the MpigE functional regions were
analyzed using the Pfam 27.0 program (http://pfam.sanger.ac. uk/). ...
New Phytologist
200: 820–833. doi: 10.1111/nph.12396
Plant Defensin type 1 (PDF1): protein promiscuity and expression variation within the Arabidopsis genus shed light on zinc tolerance acquisition in Arabidopsis halleri.
Shahzad et al.,
1Biochimie et Physiologie Moleculaire des Plantes, Unite Mixte de Recherche Montpellier, SupAgro/CNRS/INRA/Universite Montpellier II, Montpellier Cedex 1, France
2Montpellier SupAgro, UMR AGAP, Montpellier, France
... Genes were predicted using the FGENESH program (Salamov & Solovyev, 2000)
under the SOFTBERRY software (www.softberry.com) and were annotated based
on BLAST similarity searches (Altschul et al., 1990). The presence ...
Cell Stress and Chaperones
Volume 18, Issue 3 , pp 321-331 DOI:10.1007/s12192-012-0384-9
Functional relevance of J-protein family of rice (Oryza sativa)
Neelam K Sarkar, Upasna Thapar, Preeti Kundnani, Priyankar Panwar, Anil Grover
1. Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
... FGENESH analysis of genomic sequence of Os03g12236 at softberry (www.softberry.
com/) revealed presence of one gene having 10 exons coding for 462 amino acid
protein. The amino acid sequence deduced from softberry ...
Phytopathology
November 2013, Volume 103, Number 11 Pages 1162-1168 http://dx.doi.org/10.1094/PHYTO-02-13-0044-R
Fine Mapping and Identification of Blast Resistance Gene Pi-hk1 in a Broad-Spectrum Resistant japonica Rice Landrace
Wu et al.,
State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China. Y. Wu and Y. Bao contributed equally to this work.
... (http://genes.mit.edu/GENSCAN.html) and softberry (http://linux1.softberry.com/berry.phtml).
The predicted introns about 200-500bp were ... Page 7 of 28 Page 8. 8 FGENESH (http://linux1.
softberry.com/) and RiceGAAS (http://rgp.dna.affrc.go.jp) software (32). ...
Biotechnology Letters
Volume 35, Issue 9 , pp 1425-1432 DOI:10.1007/s10529-013-1219-1
Deletion of pigR gene in Monascus ruber leads to loss of pigment production
Nana Xie, Qingpei Liu, Fusheng Chen
1. College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
2. State Key Laboratory of Agricultural Microbiology, Wuhan, 430070, Hubei, China
... agitation. Three replicates of each sample were carried out. Sequence analysis. Amino
acid sequence encoded by pigR was predicted using the SoftBerry's FGENESH
program (http://linux1.softberry.com/berry.phtml). Homology ...
Heredity
(2013) 111, 57–65; doi:10.1038/hdy.2013.19; published online 3 April 2013
The discovery of Foxl2 paralogs in chondrichthyan, coelacanth and tetrapod genomes reveals an ancient duplication in vertebrates
M T Geraldo 1, G T Valente 1, A SK Braz 2 and C Martins 1
1Integrative Genomics Laboratory, Department of Morphology, Institute of Biosciences, Sao Paulo State University–UNESP, Botucatu, Sao Paulo, Brazil
2Laboratory of Computational Biology and Bioinformatics, Center of Natural and Human Sciences, Federal University of ABC–UFABC, Santo Andre, Sao Paulo, Brazil
... The sequences acquired were inserted into the online program Softberry FGENESH
(http://www.softberry.com/) using T. rubripes as the reference genome to recover the whole gene
transcriptional region and confirm the identification of genes in these syntenic regions ...
Microbiological Research
Volume 168, Issue 6, 19 July 2013, Pages 340–350 DOI: 10.1016/j.micres.2013.01.005
Identifying pathogenicity genes in the rubber tree anthracnose fungus Colletotrichum gloeosporioides through random insertional mutagenesis
Cai et al.,
a Environment and Plant Protection College, Hainan University, Danzhou, Hainan 571737, China
b Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan 571737, China
... Sixteen T-DNA integration sites of transformants impaired in pathogenicity were identified, and
in most cases T-DNA integrated into a predicted ORF of putative genes based on gene structure
prediction by FGENESH program (Softberry Inc., Mount Kisco, NY, USA, http://linux1 ...
Cell Biology International
(2013) 37: 687–693. doi: 10.1002/cbin.10080
Computational prediction and characterisation of ubiquitously expressed new splice variant of Prkaca gene in mouse.
Banday, A. R., Azim, S., Hussain, M. A., Nehar, S. and Tabish, M.
1Faculty of Life Sciences, Department of Biochemistry, A.M. University, Aligarh, Uttar Pradesh, India
2P.G. Department of Zoology, Ranchi University, Ranchi, Jharkhand, India
.. were used at HMM gene (http://www.cbs.dtu.dk/services/HMMgene) (Lukashin and Borodovsky,
1998), Genescan (http://genes.mit.edu/GENSCAN.html), GeneSplicer (http://cbcb.umd.edu/
software/GeneSplicer/) (Pertea et al., 2001), FGENESH (http://www.softberry.com/berry ...
Nucl. Acids Res.
(1 January 2013) 41 (D1): D1192-D1198.
doi: 10.1093/nar/gks1090
OrysPSSP: a comparative Platform for Small Secreted Proteins from rice and other plants
Pan et al.,
Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, 2Shanghai Center for Bioinformation Technology, Shanghai 200235 and 3Tarim University, Alar, Xinjiang 843300, China
... Constructing the starting dataset of small peptides (25–250 aa in length) by combining
data from whole-genome screening and from gene modeling using Augustus (v2.5.5)
and FGENESH (Softberry, http://www.softberry.com) (34). ...
Trends in Bioinformatics
2013, Vol. 6 Issue 3, p62-90. 29p.
In-silico Study of Transcription Factor Binding Elements of Human PAX Gene Family Members
Rashmi et al.,
... For study of cis-acting elements-4000 upstream regions were retrieved using NCBI.
Cis-acting elements analysis were done using fgenesh tool of softberry server
(http://linuX1 .softberry.com/berry.phtml; Solovyev and Salamov, 1997). ...
Genes & Genomics
Volume 35, Issue 2 , pp 159-166 DOI:10.1007/s13258-013-0075-7
Nucleotide diversity of the upstream region of the putative MADS-box gene controlling soybean maturity
Jungmin Ha, Puji Lestari, Suk-Ha Lee
1. Department of Plant Science and Research Institute for Agriculture and Life Science, Seoul National University, Seoul, 151-921, Korea
2. Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Jl. Tentara Pelajar No. 3A, Bogor, 16111, Indonesia
... BLAST algorithm. Any putative genes were also investigated with the FGENESH
software (http://linux1.softberry.com/berry.phtml) using the dicot plant option
(Arabidopsis). Primer design and PCR amplification. To amplify the ...
Physiologia Plantarum
Volume 150, Issue 1, pages 32–45, January 2014 DOI:10.1111/ppl.12064
Transcriptional regulation of the V-ATPase subunit c and V-PPase isoforms in Cucumis sativus under heavy metal stress
Katarzyna Kabala*, Malgorzata Janicka-Russak, Malgorzata Reda, Magdalena Migocka
Department of Plant Molecular Physiology, Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland
.. cucumber sequences were then analyzed using gene finding programs identifying full-length
cDNA sequences (comprising the 5? and 3? ends): GeneMark (http://exon.biology.gatech.edu/
eukhmm.cgi) and FGENESH as well as FGENESH+ on the SoftBerry server (http ...
Russian Journal of Plant Physiology
Volume 60, Issue 5 , pp 713-719 DOI:10.1134/S102144371305004X
Cloning and characterization of ethylene-insensitive 2 (EIN2) gene from Cucumis melo
F. Gao, J. Hao, Y. Yao, X. Wang, A. Hasi
1. College of Life Sciences, Inner Mongolia University, Hohhot, 010021, P.R. China
2. Inner Mongolia Key Laboratory of Herbage and Endemic Crop Biotechnology, Hohhot, 010021, P.R. China
... tigs that contain the genomic DNA sequence of the putative CsEIN2. (3) The gene prediction
program Softberry of FGENESH (http://linux1.soft berry.com/berry.phtml) was used to predict
multiple (alternative splice) variants of potential CsEIN2 genes in the cucumber genome ...
European Journal of Plant Pathology
Volume 137, Issue 1 , pp 55-65 DOI:10.1007/s10658-013-0216-5
Mining of rice blast resistance gene Pi54 shows effect of single nucleotide polymorphisms on phenotypic expression of the alleles
Kumari et al.,
1. National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Room No 39, LBS Centre, Pusa Campus, New Delhi, 110012, India
2. Division of Crop Improvement, Indian Institute of Pulses Research, Kanpur, 208 024, Uttar Pradesh, India
... Eur J Plant Pathol Page 3. using Primer 3 software (www.softberry.com). The ... Eur J
Plant Pathol Page 4. performed to predict gene structure and ORF region using
FGENESH software trained for monocot (www.softberry.com). The ...
Phil. Trans. R. Soc. B
19 September 2013 vol. 368 no. 1626 20130047 DOI:10.1098/rstb.2013.0047
Functional endogenous viral elements in the genome of the parasitoid wasp Cotesia congregata: insights into the evolutionary dynamics of bracoviruses
Bezier et al.,
1Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Universite Francois Rabelais, Parc de Grandmont, 37200 Tours, France
2Commissariat a l'Energie Atomique, Genoscope (Centre National de Sequencage), 2 rue Gaston Cremieux, CP 5706, 91057 Evry Cedex, France
... For both Cotesia spp., gene predictions were performed using a combination of FGENESH and
FGENESH+ software from the SoftBerry platform with the Apis mellifera training set
(http://linux1.softberry.com/all.htm) and from the EMBL-EBI platform using Wise2 algorithms (http ...
Theoretical and Applied Genetics
Volume 126, Issue 1 , pp 219-229 DOI:10.1007/s00122-012-1975-7
Fine mapping and characterization of BPH27, a brown planthopper resistance gene from wild rice (Oryza rufipogon Griff.)
Huang et al.,
1. State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Agricultural College, Guangxi University, Nanning, 530005, China
2. Rice Research Institute, Plant Protection Institute and Guangxi Rice Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
... The putative open reading frame (ORF) in the target region was predicted by the online
software GENESCAN and FGENESH of Softberry (www.softberry.com/berry.phtml) with
monocot plants as the model organism. Host selection behavior ...
Microbiology
October 2013 vol. 159 no. Pt 10 2169-2179 DOI:10.1099/mic.0.069542-0
CdpC2PT, a reverse prenyltransferase from Neosartorya fischeri with a distinct substrate preference from known C2-prenyltransferases
Kathrin Mundt 1,2 and Shu-Ming Li 1,2
1Institut fur Pharmazeutische Biologie und Biotechnologie, Philipps-Universitat Marburg, Deutschhausstrasse 17A, 35037 Marburg, Germany
2Zentrum fur Synthetische Mikrobiologie, Philipps-Universitat Marburg, 35032 Marburg, Germany
... al., 1988). Computer-assisted sequence analysis. For intron prediction and sequence
analysis, fgenesh (http://linux1.softberry.com) and dnasis (v. 2.1; Hitachi Software
Engineering) were used, respectively. Sequence identities ...
Molecular Genetics and Genomics
Volume 288, Issue 3-4 , pp 111-129 DOI:10.1007/s00438-013-0733-0
Genome-wide identification, phylogeny and expression analysis of SUN, OFP and YABBY gene family in tomato
Zejun Huang, Jason Van Houten, Geoffrey Gonzalez, Han Xiao, Esther van der Knaap
1. Department of Horticulture and Crop Science, The Ohio State University/OARDC, 217A Williams Hall, 1680 Madison Avenue, Wooster, OH, 44691, USA
... solgenomics.net). We identified nine genes that were not in database ITAG Release
2.3 but appear to have protein coding potential based on annotation by FGENESH
(http://linux1.softberry.com/berry.phtml). Initial evidence ...
Euphytica
December 2013 DOI:10.1007/s10681-013-1037-5
Fine mapping of the uniform immature fruit color gene u in cucumber (Cucumis sativus L.)
Yang et al.,
1. School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Minhang District, Shanghai, 200240, China
2. Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, 201602, China
... (Voorrips 2002 ). Gene prediction in the target genomic DNA regions was performed
using the program FGENESH (Salamov and Solovyev 2000 ) (http://linux1.softberry.
com/), and the results were checked manually. Results. ...
Plant and Soil
Volume 364, Issue 1-2 , pp 245-260 DOI:10.1007/s11104-012-1345-x
The genomic organization and transcriptional pattern of genes encoding nitrate transporters 1 (NRT1) in cucumber
M. Migocka, A. Warzybok, G. Klobus
1. Institute of Experimental Biology, Department of Plant Physiology, Wroclaw University, Kanonia 6/8, 50-328, Wroclaw, Poland
... AtNRT1 cDNAs were retrieved from the database and further analyzed using FGENESH and
FGENESH+ tools (Softberry, Inc., Mount Kisco, New York; www. ... The structure of each gene was
determined using FGENESH or FGENESH+ programs available on softberry.com ...
Tree Genetics & Genomes
November 2013 DOI:10.1007/s11295-013-0678-9
Cloning and functional characterization of the Rvi15 (Vr2) gene for apple scab resistance
Schouten et al.,
1. Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
2. Inova Fruit, P.O. Box 222, 4190 CE, Geldermalsen, The Netherlands
3. Plant Pathology, Institute of Integrative Biology (IBZ), ETH Zurich, Universitatstrasse 2, 8092, Zurich, Switzerland
... 2010b) was copied from the NCBI database (accession number GU295057.1). The
Vr2-A, Vr2-B, and Vr2-C amino acid sequences in GMAL 2473 were predicted by means
of the publicly available software FGENESH from SoftBerry. ...
Applied Biochemistry and Biotechnology
Volume 169, Issue 3 , pp 941-949 DOI:10.1007/s12010-012-0048-3
Molecular Cloning and Expression of a Novel b-Glucosidase Gene from Phialophora sp. G5
Xuejun Li et al.,
1. Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People’s Republic of China
2. Beijing Challenge Bio-Technology Co., Ltd., Beijing, 100081, People’s Republic of China
... designed on the assembled sequence. Sequence Analysis The introns, exons, and
transcription initiation sites were analyzed by FGENESH (http:// www.softberry.com/
berry.phtml/). Amino acid and nucleotide sequence alignments ...
Immunogenetics
Volume 65, Issue 7 , pp 531-541 DOI:10.1007/s00251-013-0692-y
IgH loci of American alligator and saltwater crocodile shed light on IgA evolution
Susana Magadan-Mompo, Christian Sanchez-Espinel, Francisco Gambon-Deza
1. Servicio Gallego de Salud (SERGAS) Unidad de Inmunologia, Hospital do Meixoeiro, Carretera de Madrid s/n, Vigo, 36210, Pontevedra, Spain
3. Oceanographic Center of Vigo, Spanish Institute of Oceanography (IEO), Subida a Radio Faro 50, 36390, Vigo, Pontevedra, Spain
... Exons coding for the CH immunoglobulin domains were identified by aligning genomic and
predicted amino acid sequences with previously published reptile immunoglobu- lin sequences.
Limits were deduced using the FGENESH (www.softberry.com) (Solovyev et al. ...
Applied Microbiology and Biotechnology
Volume 97, Issue 4 , pp 1649-1660 DOI:10.1007/s00253-012-4130-0
Identification of a brevianamide F reverse prenyltransferase BrePT from Aspergillus versicolor with a broad substrate specificity towards tryptophan-containing cyclic dipeptides
Suqin Yin, Xia Yu, Qing Wang, Xiao-Qing Liu, Shu-Ming Li
1. College of Life Sciences, Capital Normal University, No.105 Xisanhuan Beilu, Beijing, 100048, China
2. Institut fur Pharmazeutische Biologie und Biotechnologie, Philipps-Universitat Marburg, Deutschhausstrasse 17A, 35037, Marburg, Germany
... Computer-assisted sequence analysis FGENESH (Softberry, Inc.) and the DNASIS
software pack- age (version 2.1: Hitachi Software Engineering, San Bruno, CA) were
used for intron prediction and sequence analysis, respectively. ...
PloS one
July 09, 2013DOI: 10.1371/journal.pone.0068260
A Superfamily of DNA Transposons Targeting Multicopy Small RNA Genes
Kenji K. Kojima, Jerzy Jurka
Genetic Information Research Institute, Mountain View, California, United States of America
... copies. Exon-intron boundaries were predicted with the aid of SoftBerry FGENESH:
(http://linux1.softberry.com/berry.phtml??topic=fgenesh&group=programs&subgroup=
gf?ind) and GENEID (http://genome.crg.es/geneid.html). ...
International Journal of Genomics and Proteomics
Volume 4, Issue 1, 2013, pp.-64-71 Available online at http://www.bioinfopublication.org/jouarchive.php?opt=&jouid=BPJ0000227
MOLECULAR MODELING OF ?-AMYLASE FROM GERMINATED SOYBEAN (Glycine max) AND
ITS FUNCTIONAL DIVERSITY
KUMARI A. 1, SINGH V.K. 2 AND KAYASTHA A.M. 1
1School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi-221 005, UP, India.
2Centre for Bioinformatics, School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi-221 005, UP, India.
... It showed similarity with Glycine max strain Wil- liams 82 clone GM_WBb0115J10
(AC235387.1). Full length gene prediction was done for obtained strain using Fgenesh (http://
sun1.softberry.com/berry.phtml) and -1000 upstream region was retrieved for promoter study ...
Food Chemistry
Volume 141, Issue 3, 1 December 2013, Pages 2974–2981 DOI:10.1016/j.foodchem.2013.05.132
High-yield production of a low-temperature-active polygalacturonase for papaya juice clarification
Tao Tu et al.,
a Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
b Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
... Multiple alignments of protein sequences were performed using the ClustalW program
(http://www.ebi.ac.uk/clustalW/). Transcription initiation sites, intron, and exon were predicted
using the online software FGENESH (http://linux1.softberry.com/berry.phtml/). ...
Immunogenetics
Volume 65, Issue 5 , pp 387-396 DOI:10.1007/s00251-013-0678-9
Immunoglobulin light chains in medaka (Oryzias latipes)
Susana Magadan-Mompo, Anastasia M. Zimmerman, Christian Sanchez-Espinel, Francisco Gambon-Deza
1. Virologie et Immunologie Moleculaires, Institut National de la Recherche Agronomique (INRA), Domaine de Vilvert, 78352, Jouy-en-Josas, France
2. Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA
... 2009; Zimmerman et al. 2008; Bao et al. 2010). Boundaries of exons were deduced
using the software packages FGENESH (www.softberry.com) (Solovyev et al. 2006)
and Augustus (http://augustus.gobics.de/submission) (Stanke et al. ...
Mol Biol Rep.
2013 Mar;40(3):2645-62. doi: 10.1007/s11033-012-2351-z. Epub 2012 Dec 15.
Genome-wide identification, classification, and expression analysis of CDPK and its closely related gene families in poplar (Populus trichocarpa).
Genome-wide identification, classification, and expression analysis of CDPK and its closely related gene families in poplar (Populus trichocarpa). et al.,
CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and BioProcess Technology, Chinese Academy of Sciences, Qingdao, Shandong, People's Republic of China.
... Local blast was performed using Arabid- opsis CDPK and its closely related kinase proteins as
queries for the identification of genes from Populus. Manual reanno- tation was also performed
using online web server FGENESH (http://linux1.softberry.com/berry.phtml). ...
Process Biochemistry
Volume 48, Issue 12, December 2013, Pages 1879–1885 DOI:10.1016/j.procbio.2013.08.020
A novel thermophilic xylanase from Achaetomium sp. Xz-8 with high catalytic efficiency and application potentials in the brewing and other industries
Zhao et al.,
a Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
b College of Life Science, Capital Normal University, Beijing 100048, PR China
... Genes, introns, exons and transcription initiation site were predicted using the online software
FGENESH (http://linux1.softberry.com/berry.phtml). The signal peptide was predicted using
SignalP 4.1 Server (http://www.cbs.dtu.dk/services/SignalP/). ...
Plant Molecular Biology Reporter
October 2013 DOI:10.1007/s11105-013-0666-0
Molecular Cloning and Characterization of a Novel Polygalacturonase Gene, BcMF24, Involved in Pollen Development of Brassica campestris ssp. chinensis
Youjian Yu, Meiling Lv, Ying Liang, Xingpeng Xiong, Jiashu Cao
1. Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
... Full CDS sequences were analyzed by FGENESH (http://linux1.softberry.com/berry.phtml?topic=
fgenesh&group=programs&subgroup=gfind), and the molecular characteristic of the deduced
protein was viewed on the ExPASy (http://web.expasy.org/compute_pi/). ...
J. Agric. Food Chem.,
2013, 61 (28), pp 6880–6889DOI: 10.1021/jf4001296
Two Family 11 Xylanases from Achaetomium sp. Xz-8 with High Catalytic Efficiency and Application Potentials in the Brewing Industry
Zhao et al.,
† Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People’s Republic of China
‡ College of Life Science, Capital Normal University, Beijing 100048, People’s Republic of China
... Genes, introns, exons, and transcription initiation sites were predicted using the online
software FGENESH (http://linux1.softberry.com/berry.phtml). The signal peptide was predicted
using SignalP 4.0 Server (http://www.cbs.dtu.dk/services/SignalP/). ...
Applied Microbiology and Biotechnology
Volume 97, Issue 18 , pp 8121-8128 DOI:10.1007/s00253-012-4656-1
A family 5 b-mannanase from the thermophilic fungus Thielavia arenaria XZ7 with typical thermophilic enzyme features
Lu et al.,
1. Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing, 100081, People’s Republic of China
2. College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 3000457, People’s Republic of China
... nih.gov/gorf/gorf/gorf.html). The sequence assembly was per- formed using the Vector NTI
Advance 10.0 software (Invitrogen). Genes, introns, exons, and transcription initia- tion sites were
predicted using the online software FGENESH (http://linux1.softberry.com/berry.phtml). ...
Mycorrhiza
Volume 23, Issue 7 , pp 573-584 DOI:10.1007/s00572-013-0498-7
The reduced mycorrhizal colonisation (rmc) mutation of tomato disrupts five gene sequences including the CYCLOPS/IPD3 homologue
Larkan et al.,
1. School of Plant Biology M090, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, Western Australia, 6009, Australia
2. Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N0X2, Canada
3. Donald Danforth Plant Science Centre, 975 N Warson Rd, St Louis, MO, 63132, USA
... Page 6. Genes within this sequence were predicted using FGENESH software (softberry.com). ...
FGENESH gene prediction software (softberry.com) was used to annotate the region and to
determine whether any match to known mycorrhiza-regulating genes could be identified. ...
Eukaryotic Cell
September 2013 vol. 12 no. 9 1214-1224 DOI:10.1128/EC.00159-13
Unraveling the Molecular Basis of Temperature-Dependent Genetic Regulation in Penicillium marneffei
Yang et al.,
Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USAa
Department of Microbiology, University of Hong Kong, Hong Kongb
Center for Clinical Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
... Genes with a false discovery rate (FDR) of <0.05 as reported by all three packages were
considered to be differentially expressed. Gene prediction and identification of orthologs.Ab initio
gene predictions were performed using FGENESH (SoftBerry, Mount Kisco, NY). ...
Crop and Pasture Science
DOI:10.1071/CP13140
Isolation and characterisation of cytosolic glutamine synthetase (GSe) genes and association with grain protein content in durum wheat
Gadaleta et al.,
A Department of Soil, Plant and Food Sciences, Section of Genetics and Plant Breeding, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A – 70126 Bari, Italy.
... Genes prediction was conducted with the FGENESH program (http://linux1.softberry.com/berry.
phtml?topic=fgenes handgroup=programsandsubgroup=gfind). Consensus exon/ introns
boundaries were confirmed using grass expressed sequence tag sequences aligned to the ...
Appl. Environ. Microbiol.
March 2013 vol. 79 no. 6 2038-2047 DOI:10.1128/AEM.03334-12
Characterization of the Biosynthetic Genes for 10,11-Dehydrocurvularin, a Heat Shock Response-Modulating Anticancer Fungal Polyketide from Aspergillus terreus
Xu et al.,
aNatural Products Center, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, The University of Arizona, Tucson, Arizona, USA
bInstitut fur Chemie, Technische Universitat Berlin, Berlin, Germany
... earlier (17). Hidden Markov model (HMM)-based gene models were built with
FGENESH (Softberry) with additional exon/intron boundary refinements in
SPLICEVIEW (http://zeus2.itb.cnr.it/?webgene/wwwspliceview.html). The ...
IJEB
Vol.51(12) [December 2013] pp. 1130-1136
Molecular cloning and mRNA expression profile of Sucrose Transporter Gene BnSUT1C from Brassica napus L.
Li et al.,
... suite (Windows version 5.0.2; DNASTAR, Madison, Wis.). The complete open reading
frame (ORF) was identified with program FGENESH (http://www.softberry.com/berry.
phtml). Primers were designed in the predicted 5' and ...
Advanced BioTech
Volume:12 Issue:11 May 10, 2013
Isolation and in silico Depiction of Novel R2-R3 MYB Transcription Factors from Sugarcane
Pranali A. Kulkarni1, Prabu G.R. and Rachayya M. Devarumath
1. Molecular Biology & Genetic Engineering Division, Vasantdada Sugar Institute, Manjari (Bk.), Tal. Haveli, Pune-412307, Maharashtra, India.
2. Department of Biotechnology, University of Pune, Pune-411005, Maharashtra, India.
3. Department of Biotechnology, School of Life Sciences, Karpagam University, Pollachi Coimbatore – 641021, Tamil Nadu, India.
... The nucleotide sequences of SbMYB18 and SoMYB18 were processed for deducing
the exon and intron pattern online using fGENESH Hidden Markov Model (HMM) based
gene structure prediction tool (www.softberry.com/berry.phtml). ...
Plant Molecular Biology Reporter
Volume 31, Issue 6 , pp 1249-1260 DOI:10.1007/s11105-013-0585-0
Structure, Evolution, and Expression of the b-Galactosidase Gene Family in Brassica campestris ssp. chinensis
Jinlong Liu, Minghui Gao, Meiling Lv, Jiashu Cao
1. Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
... Each of the BGAL gene loci in Arabidopsis was used to obtain all possible BGAL genes in B.
campestris from BRAD (Table 1). Each predicted BGAL gene sequence in B. campestris was
confirmed by FGENESH (http://www.softberry.com/berry.phtml?topic=fgenesh). ...
PloS one
May 28, 2013DOI: 10.1371/journal.pone.0064432
Adaptive Selection on Bracovirus Genomes Drives the Specialization of Cotesia Parasitoid Wasps
Jancek et al.,
Institut de Recherches sur la Biologie de l’Insecte, UMR 7261 CNRS, Universite Francois-Rabelais, UFR Sciences et Techniques, Parc Grandmont, Tours, France
aboratoire Evolution, Genomes et Speciation, CNRS UPR9034, IRD UR 072 and Universite Paris Sud, Gif sur Yvette, France, Unite de Recherche UMR 1272, Physiologie de l’Insecte, Signalisation et Communication, INRA, Versailles, France
... Gene predictions on CskBV newly sequenced contigs and BACs and on CsmBV BACs were
made with SoftBerry's FGENESH de novo prediction tool [37] and FGENESH+ using the honeybee
(Apis mellifera L.) training set and were manually corrected by comparison with ...
Molecular Immunology
Volume 56, Issue 4, 31 December 2013, Pages 745–756 DOI:10.1016/j.molimm.2013.07.012
Accessory molecules for Toll-like receptors in Teleost fish. Identification of TLR4 interactor with leucine-rich repeats (TRIL)
Danilo Pietretti a, Herman P. Spaink b, Alberto Falco a, Maria Forlenza a, Geert F. Wiegertjes a,
a Cell Biology and Immunology Group, Wageningen Institute of Animal Sciences, Wageningen University, PO Box 338, 6700 AH Wageningen, The Netherlands
b Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
... al., 2012). Genomic information was then used to predict nucleotide and protein
sequences using FGENESH version 2.5 (www.softberry.com). Table 1. Accessory
molecules present in teleost fish species. Accessory molecules ...
Theoretical and Applied Genetics
October 2013 DOI:10.1007/s00122-013-2205-7
A putative candidate for the recessive gall midge resistance gene gm3 in rice identified and validated
Sama et al.,
1. Directorate of Rice Research, Rajendranagar, Hyderabad, 500030, Andhra Pradesh, India
2. International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502324, Andhra Pradesh, India
... The down- loaded sequences were then analyzed using the software package FGeneSH
(http://www.softberry.com) for open reading frames (OrFs) and annotated using BlAST-P utility
(http://www.ncbi.nlm.nih.gov) to identify the puta- tive function of each gene present in the ...
Plant Cell Reports
November 2013, DOI:10.1007/s00299-013-1535-x
Transcriptional regulation of early embryo development in the model legume Medicago truncatula
Sergey Kurdyukov, Youhong Song, Michael B. Sheahan, Ray J. Rose
1. Australian Research Council Centre of Excellence for Integrative Legume Research, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
2. Kolling Institute of Medical Research, Kolling Building, Royal North Shore Hospital, St Leonards, NSW, 2065, Australia
... The corresponding gene loci and protein sequences were obtained from the Mt3.5
genome release (http://www.medicagohapmap.org), or where unavailable, they were
predicted directly using FGENESH (http://www.softberry.com). ...
J Hered
(2013) 104 (1): 134-139. doi: 10.1093/jhered/ess075
Localization of a New Gene for Bitterness in Cucumber
Zhang et al.,
From the Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 10081 China (Zhang, Miao, Sun, Wang, Huang, and Gu); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner).
... Gene prediction was performed with the computer program BGF (http://bgf.genomics.org.cn) and
verified by FGENESH (http://sunl.softberry.com/) (Salamov and Solovyev 2000), GENESCAN
(http://genes.mit.edu/GENSCAN.html) (Burge and Karlin 1997), TwinScan (http://mblab ...
Arthropod-Plant Interactions
Volume 7, Issue 4 , pp 389-402 DOI:10.1007/s11829-013-9253-4
Hessian fly larval attack triggers elevated expression of disease resistance dirigent-like protein-encoding gene, HfrDrd, in resistant wheat
Subhashree Subramanyam, Cheng Zheng, John T. Shukle, Christie E. Williams
1. Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
2. Novartis Pharmaceuticals Corporation, East Hanover, NJ, 07936, USA
... subcellular localization of HFRDRD proteins. Structural analysis of the genomic sequence
was performed using the FGENESH program (http://linux1.softberry.com/berry.phtml).
Phylogenetic analysis. In order to explore the evolutionary ...
Microbial Pathogenesis
Volume 64, November 2013, Pages 6–17 DOI:10.1016/j.micpath.2013.06.001
Identification of virulence genes in the crucifer anthracnose fungus Colletotrichum higginsianum by insertional mutagenesis
Liu et al.,
a The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
b School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
c Department of Biology, University of Saskatchewan, Saskatoon S7N 5E2, Canada
... algorithm of the Basic Local Alignment Search Tool [25] hosted by the National Center for
Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov), and open reading frames were
further analyzed using the gene prediction program FGENESH (Softberry Inc., Mount Kisco ...
Planta
Volume 238, Issue 2 , pp 293-305 DOI:10.1007/s00425-013-1891-3
Analysis of nucleotide diversity among alleles of the major bacterial blight resistance gene Xa27 in cultivars of rice (Oryza sativa) and its wild relatives
Bimolata et al.,
1. Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad, 500046, India
2. Crop Improvement Section, Directorate of Rice Research, Rajendranagar, Hyderabad, 500030, India
... Based on the sequences obtained from the genotypes under study, the coding regions
and the UTR regions of the new alleles were predicted through the software utility,
FGENESH (http://www.softberry.com) (Salamov and Solovyer 2000 ). ...
G3
March 1, 2013 vol. 3 no. 3 563-572 DOI:10.1534/g3.113.005587
Fine-Mapping and Identification of a Candidate Gene Underlying the d2 Dwarfing Phenotype in Pearl Millet, Cenchrus americanus (L.) Morrone
Parvathaneni et al.,
*Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia 30602
†Department of Crop and Soil Sciences, University of Georgia, Athens, Georgia 30602
... respectively. The sequence of BAC 293B22 has been deposited in GenBank under
accession number KC463796. Gene prediction was performed using FGENESH
with the monocot training set (www.softberry.com). Repetitive ...
Theoretical and Applied Genetics
Volume 126, Issue 10 , pp 2643-2653 DOI:10.1007/s00122-013-2162-1
Fine mapping of the Ph-3 gene conferring resistance to late blight (Phytophthora infestans) in tomato
Zhang et al.,
1. The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancunnandajie 12, Beijing, 100081, People’s Republic of China
2. Wageningen UR Plant Breeding, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
... MapQTl 4.0 (Van Ooijen and Maliepaard 1996) was used to perform the QTl analysis. Gene
prediction and sequence analysis The online program FGeneSH was used to pre- dict open
reading frames (OrFs) in the target region (http://linux1.softberry.com/). ...
PloS one
September 24, 2013DOI: 10.1371/journal.pone.0075544
Dynamic Evolution of Rht-1 Homologous Regions in Grass Genomes
Wu et al.,
Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, China
Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, China
... Repeats/ gene_annotation.pdf). Here, gene predictions were performed mainly by
using the program FGENESH with training sets of the monocots including maize,
rice, wheat and barley (http://www.softberry.com). In addition ...
Heredity
110, 570-577 (June 2013) | doi:10.1038/hdy.2013.2
Diversity and abundance of the abnormal chromosome 10 meiotic drive complex in Zea mays
Kanizay et al.,
... Masked contigs were then mapped with BLAST to the non-redundant nucleotide and protein
databases at NCBI with an e-value cutoff of 10 ?5 (Supplementary Table 2). Gene models were
identified using FGenesH (SOFTBERRY) and Augustus (http://bioinf.uni-greifswald.de ...
BMC Genomics.
2013; 14: 169. DOI:10.1186/1471-2164-14-169
Transcriptome analysis of pigeon milk production – role of cornification and triglyceride synthesis genes
Gillespie et al.,
Australian Animal Health Laboratory, CSIRO Animal, Food and Health Sciences, 5 Portarlington Road, Geelong, Victoria, Australia
2School of Life and Environmental Sciences, Deakin University, Pigdons Road, Geelong, Victoria 3216, Australia
...The scaffolds of interest were then submitted to a Hidden Markov Model gene prediction program
(FGENESH, Softberry; http://linux1.softberry.com/berry.phtml) using parameters for chicken (aves) to identify predicted full-length gene sequences. Where scaffolds were too large to be processed by FGENESH, the region of the scaffold with the BLAST match was submitted....
Molecular Biology Reports
Volume 40, Issue 2 , pp 1385-1396 DOI:10.1007/s11033-012-2182-y
Characterization of the NADP-malic enzymes in the woody plant Populus trichocarpa
Yu et al.,
1. State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
... We performed the PtNADP-ME4 gene structure (exons and introns) prediction using the
FGENESH program on the SoftBerry server (http://www.soflberry.corn/berry.phtml), and
present new predicted PtNADP-ME4 gene sequences (Table S1). ...
Front Plant Sci.
2013; 4: 318. DOI:10.3389/fpls.2013.00318
A comparison of the molecular organization of genomic regions associated with resistance to common bacterial blight in two Phaseolus vulgaris genotypes
Perry et al.,
1Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
2Department of Biological Sciences, University of Windsor, Windsor, ON, Canada
...The sequence data was examined for open reading frames using FGENESH (http://www.softberry.org), with the Medicago gene model....
New Phytologist
197: 595–605. doi: 10.1111/nph.12043
The Brassica napus blackleg resistance gene LepR3 encodes a receptor-like protein triggered by the Leptosphaeria maculans effector AVRLM1.
Larkan et al.,
1Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
2School of Plant Biology, University of Western Australia, Crawley, WA, Australia
3The UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
... Identification, cloning and transformation of candidate gene. A B. rapa BAC spanning the
LepR3 interval was annotated for gene content using fgenesh software (www.softberry.
com) trained to 'Dicot plants (Arabidopsis)' to predict gene content. ...
Theoretical and Applied Genetics
Volume 126, Issue 8 , pp 2187-2196 DOI:10.1007/s00122-013-2128-3
Fine mapping of the pleiotropic locus B for black spine and orange mature fruit color in cucumber identifies a 50 kb region containing a R2R3-MYB transcription factor
Yuhong Li, Changlong Wen, Yiqun Weng
1. Horticulture College, Northwest A&F University, Yangling, 712100, China
2. Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
... with preceding fragment. Gene prediction in target genomic DNA regions was
performed with the computer program FGENESH (Salamov and Solovyev 2000)
(http://sunl.softberry.com/) and checked manually. Candidate gene ...
The Plant Cell
July 2013 vol. 25 no. 7 2536-2544 DOI:10.?1105/?tpc.?113.?111856
Formation and Expression of Pseudogenes on the B Chromosome of Rye
Ali Mohammad Banaei-Moghaddam, Karla Meier, Raheleh Karimi-Ashtiyani and Andreas Houben 1
Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
... Therefore, the genomic sequences of all fragments were BLASTed against the rye EST
database (Haseneyer et al., 2011) and analyzed using FGENESH software
(http://linux1.softberry.com/berry.phtml) (see Supplemental Figure 1 online). ...
Front Plant Sci.
2013; 4: 258. DOI:10.3389/fpls.2013.00258
Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture—insights from genomics
Studholme et al.,
1Biosciences, Molecular Plant Pathology, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
2Plant Biology and Crop Science, Rothamsted Research, Harpenden, UK
Edited by: Corne M. J. Pieterse, Utrecht University, Netherlands
... (1991). Bioinformatics methods. We used Velvet version 1.1.04 (Zerbino and Birney, 2008)
for de novo assembly of genome sequence. For ab initio gene prediction we used FgenesH
(http://linux1.softberry.com/berry.phtml?topic=fgenesh). ...
Plant Science
Volume 210, September 2013, Pages 241–249 DOI:10.1016/j.plantsci.2013.06.003
Mutation of OsDET1 increases chlorophyll content in rice
Huang et al.,
a Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400030, China
b Institute of Rice, Chongqing Academy of Agricultural Sciences, Chongqing, China
... mapped to a 87-kb DNA region (Fig. 1a). Eight annotated candidate genes were located
in the DNA region using the program FGENESH 2.2 (www.softberry.com). Further
amplification of the relevant DNA fragments and sequence ...
G3
January 1, 2013 vol. 3 no. 1 41-63 doi: 10.1534/g3.112.004044
Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence
Manning et al.,
*Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
†Department of Forest Sciences, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4
‡Carbone/Ferguson Laboratories, Division of Neuroscience, Oregon National Primate Research Center (ONPRC), Beaverton, Oregon 97006
...Protein-encoding genes were annotated using a combination of manual curation, EST alignments, and ab initio gene predictions made by
FGENESH, FGENESH+ (http://linux1.softberry.com) and GENEID (http://genome.crg.es/software/geneid). ...
Physiological and Molecular Plant Pathology
Volume 84, October 2013, Pages 76–85 DOI:10.1016/j.pmpp.2013.07.007
Foatf1, a bZIP transcription factor of Fusarium oxysporum f. sp. cubense, is involved in pathogenesis by regulating the oxidative stress responses of Cavendish banana (Musa spp.)
Xingzhu Qi b, Lijia Guo a, c, Laying Yang a, c, Junsheng Huang a, c,
a Institute of Environment and Plant Protection, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
b College of Agriculture Hainan University, Haikou 570228, China
c Key Laboratory of Monitoring and Control of Tropical Agricultural and Forest Invasive Alien Pests, Ministry of Agriculture, Haikou 571101, China
... The protein-encoding gene sequence was submitted to a gene-finding program (FGENESH A,
Softberry Inc.) to perform automated annotation and obtain the putative mRNA sequence of Foatf1.
The PCR primers were designed based on the putative mRNA sequence of Foatf1. ...
PloS one
December 16, 2013DOI: 10.1371/journal.pone.0082353
Mating Type Locus of Chinese Black Truffles Reveals Heterothallism and the Presence of Cryptic Species within the T. indicum Species Complex
Beatrice Belfiori, Claudia Riccioni, Francesco Paolocci, Andrea Rubini
Institute of Biosciences and BioResources - Perugia Division, National Research Council, Perugia, Italy
... www.geneious.com). Gene prediction analyses were performed using FGENESH
(http://linux1.softberry.com/berry.phtml). RNA Isolation and Reverse-transcription
Polymerase Chain Reaction Analysis. Total RNA was isolated ...
Plant Disease
February 2013, Volume 97, Number 2 Pages 245-251 http://dx.doi.org/10.1094/PDIS-11-11-0941-RE
Chromosomal Mapping and QTL Analysis of Resistance to Downy Mildew in Cucumis sativus
S. P. Zhang et al.,
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
... Gene prediction was performed with the computer program BGF (http://bgf.genomics.org.cn) and
veriWed by FGENESH (http://linuxl.softberry.com/) (40), GENESCAN (http://genes.mit.edu/
GENSCAN.html) (4), TwinScan (http:// mblab.wustl.edu/software/download/) (24), and then ...
Phytopathology
June 2013, Volume 103, Number 6 Pages 594-599 http://dx.doi.org/10.1094/PHYTO-10-12-0260-R
Functional Analysis of Pid3-A4, an Ortholog of Rice Blast Resistance Gene Pid3 Revealed by Allele Mining in Common Wild Rice
Qiming Lv et al.,
Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
... 9-bp deletion, in addition to many SNPs, compared with that of Pid3. According to the computer
program FGENESH (http://www.softberry.com), the two genes should have predicted promoter
regions beginning 900-bp from their respective start codons, ...
BMC Plant Biology
2013, 13:162 doi:10.1186/1471-2229-13-162
Combined linkage and association mapping reveals candidates for Scmv1, a major locus involved in resistance to sugarcane mosaic virus (SCMV) in maize
Tao et al.,
1 National Maize Improvement Center, China Agricultural University, 2 West Yuanmingyuan Road, Beijing 100193, People’s Republic of China
2 Department of Agronomy, Iowa State University, 1204 Agronomy Hall, Ames, Iowa 50011, USA
3 Research Center Flakkebjerg, University of Aarhus, 4200, Slagelse, Denmark
... We used Fgenesh software (http://linux1.softberry.com/berry.phtml, version 2.6) to predict ten
putative genes from the masked sequence, including seven genes with putative functions, two
hypothetical genes, and one gene without significant similarity to known genes (Figure 3C ...
J Hered
(2013) 104 (2): 273-286. doi: 10.1093/jhered/ess102
Identification and Characterization of a Homologue to the Arabidopsis INDEHISCENT Gene in Common Bean
Tania Gioia, Giuseppina Logozzo, James Kami, Pierluigi Spagnoletti Zeuli and Paul Gepts
From the Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Universita degli Studi della Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy (Gioia, Logozzo, Spagnoletti Zeuli); and the Department of Plant Sciences/MS1, University of California, 1 Shields Avenue, Davis, CA 95616–8780 (Kami and Gepts).
... with AtIND. Gene structure was predicted using the software FGENESH
(http://linux1.softberry.com/berry.phtml), whereas the search for ORFs was performed
using ORF finder (http://www.ncbi.nlm.nih.gov/projects/gorf/). To identify ...
J. Exp. Bot.
(2013) 64 (2): 651-663. doi: 10.1093/jxb/ers363
Identification of differentially methylated regions during vernalization revealed a role for RNA methyltransferases in bolting
Hebrard et al.,
1 Universite d’Orleans, UFR/Faculte des Sciences, UPRES EA 1207 Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328 ARCHE, rue de Chartres, BP6759, 45067 Orleans cedex 2, France
2 SESVanderHave N.V./S.A., Soldatenplein Z2 nr15, Industriepark, B-3300 Tienen, Belgium
... The identification of potential transposable elements (TEs) in the RLGS genomic sequences
was realized by the identification of potential coding sequences (FGENESH on http://linux1.
softberry.com/berry.phtml) followed by BLASTP analysis and the search of dispersed ...
Ann Bot
(2013) 111 (2): 305-315. doi: 10.1093/aob/mcs260
A triallelic genetic male sterility locus in Brassica napus: an integrative strategy for its physical mapping and possible local chromosome evolution around it
Lu et al.,
1National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement (Ministry of Agriculture), Huazhong Agricultural University, Wuhan 430070, China
2Dandong Academy of Agricultural Sciences, Fengcheng 118109, P.R. China
... Polymerase (Finnzymes Oy, Espoo, Finland). The website-based software FGENSH
(http://www.softberry.com) was employed to predict the putative open reading frames
(ORFs) located in the target region. The Plant Repeat Databases ...
Molecular Genetics and Genomics
December 2013 DOI:10.1007/s00438-013-0795-z
A systematic exploration of high-temperature stress-responsive genes in potato using large-scale yeast functional screening
Baniekal Hiremath Gangadhar, Jae Woong Yu, Kappachery Sajeesh, Se Won Park
1. Department of Molecular Biotechnology, Konkuk University, Seoul, 143701, South-Korea
... FGeneSH (http://linux1.softberry.com/berry.phtml?topic=fgenesh &group=programs&subgroup=
gfind) was used for those sequences for which we could not able to find possible OrF using
GenSCan (Burge and Karlin 1998; Salamov and Solovyev 2000). ...
Crop Science
27 Nov. 2013; doi: 10.2135/cropsci2013.09.0598
Fine Mapping of the Cross-incompatibility Locus Gametophytic Factor 1 (ga1) Using a Homogeneous Maize Population 2
Liu et al.,
1 State Key Laboratory of Crop Biology, Shandong Agricultural University, Daizong Street 61, Taian, Shandong, 271018, CHINA
2 College of Life Science, Shandong University, Shanda South Street 27, Jinan, 250100, CHINA
... polyacrylamide gel and visualized with ethidium bromide staining. The maize gene 18 set
(www.maizeequence.org) and website-based software FGENSH 19 (http://www.softberry.com)
was applied to predict and filter the putative genes from 20 the mapping interval. 21 22 ...
Appl. Environ. Microbiol.
June 2013 vol. 79 no. 12 3770-3778 DOI:10.1128/AEM.03833-12
Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens
Aylward et al.,
Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USAa
Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USAb
... Amino acid sequences for the nucleotide sequences of these CAZyme genes were
obtained using a combination of 6-frame translation, the software program FGENESH
(Softberry), and BLASTX (27) against the NCBI NR database (44). ...
New Phytologist
197: 416–430. doi: 10.1111/nph.12026
Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body DNA methylation in open chromatin state.
Lafon-Placette et al.,
1Universite d'Orleans, Faculte des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Orleans, France
2INRA, USC1328 Arbres et Reponses aux Contraintes Hydriques et Environnementales (ARCHE), Orleans, France
... Identification of transposase was performed using Fgenesh software (http://linux1.softberry.com/
berry.phtml?topic=fgenesh&group=programs&subgroup=gfind) and confirmed by TBlastX
analysis (e-value < 10 ?30 ) on a flowering plant transcripts database. ...
Genetics
September 1, 2013 vol. 195 no. 1 263-273 DOI:10.1534/genetics.113.152330
Cloning and Characterization of a Critical Regulator for Preharvest Sprouting in Wheat
Liu et al.,
*Department of Agronomy, Kansas State University, Manhattan, Kansas 66506
†Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506
‡Faculty of Science, Genomics and Biotechnology Section, Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
... Bobwhite as control. Bioinformatics and statistical analysis. Genomic sequences
from the three BACs covering the Qphs.pseru-3AS region were annotated using
FGENESH (http://linux1.softberry.com/berry.phtml). The promoter ...
New Phytologist
200: 675–690. doi: 10.1111/nph.12414
A metabolic gene cluster in Lotus japonicus discloses novel enzyme functions and products in triterpene biosynthesis
Krokida et al.,
1Department of Biochemistry and Biotechnology, University of Thessaly, Larisa, Greece
2Department of Metabolic Biology, John Innes Centre, Norwich, UK
3Unidad de Biotecnologia, Centro de Investigacion Cientifica de Yucatan, Merida, Yucatan, Mexico
... A region of c. 300 kb flanking each side of the OSC genes was screened and analysed using
FGENESH gene prediction software (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=
programs&subgroup=gfind) and GeneScanwebserver (Burge & Karlin, 1998). ...
BMC Genomics
2013, 14:683 doi:10.1186/1471-2164-14-683
A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids
Davey et al.,
1 Laboratory of Fruit Breeding and Biotechnology, Division of Crop Biotechnics, Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, box 2427B-3001, Heverlee, Leuven, Belgium
2 Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
... B-genome annotation. Ab initio gene prediction was carried out using the FGENESH
software, available online from http://linux1.softberry.com/all.htm webcite and using
the default parameters and the 'monocot model plant' parameters. ...
Acta Physiologiae Plantarum
Volume 35, Issue 2 , pp 483-500 DOI:10.1007/s11738-012-1091-y
Analysis of the expression, subcellular and tissue localisation of phosphoglucan, water dikinase (PWD/GWD3) in Solanum tuberosum L.: a bioinformatics approach for the comparative analysis of two ?-glucan, water dikinases (GWDs) from Solanum tuberosum L.
Orzechowski et al.,
1. Department of Biochemistry, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
2. Department of Biometrics and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
... Identification of the coding region, open reading frames and the translation of the StGWD3 nucleotide sequence was based on the
FGENESH gene structure prediction based on the Hidden Markov Model (HMM) constructed for Nicotiana tabacum (Solanaceae) genome (http://?linux1.?softberry.?com/?berry.?phtml). ...
Plant Molecular Biology Reporter
Volume 32, Issue 1 , pp 28-41 DOI:10.1007/s11105-013-0597-9
Genome-Wide Identification, Classification, Expression Profiling, and SSR Marker Development of the MADS-Box Gene Family in Citrus
Hou et al.,
1. Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
... pseudogenes or incorrect annotations because of the lack of a start or stop codon in the open
reading frame, and manual reannotation was performed to correct and reannotate the putative
MADS-box using an online web server FGENESH (http://linux1.softberry.com/ berry.phtml ...
Planta
Volume 237, Issue 1 , pp 279-292 DOI:10.1007/s00425-012-1756-1
Young Leaf Chlorosis 1, a chloroplast-localized gene required for chlorophyll and lutein accumulation during early leaf development in rice
Zhou et al.,
1. National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
2. National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
... P0027G10. Within this region, five ORFs were predicted using the program FGENESH
2.2 (http://www. softberry.com) (Fig. 2b). To determine the mutation site, all five cDNA
sequences were separately isolated from young leaves. ...
Fungal Diversity
May 2013, Volume 60, Issue 1, pp 161-170, DOI:10.1007/s13225-013-0228-7
Getting to the bottom of Taxol biosynthesis by fungi
Uwe Heinig, Susanne Scholz, Stefan Jennewein
1. Fraunhofer Institut fur Molekularbiologie und Angewandte Okologie, Forckenbeckstrasse 6, 52074, Aachen, Germany
... Sequence analysis Sequences were analyzed using CLC Combined Workbench v3.6.1,
Lasergene 7 Package, NCBI Blast and CloneManager Professional Suite 8. FGENESH
was use for ORF and protein prediction (http://linux1.softberry.com/). ...
Journal of Plant Interactions
Volume 8, Issue 1, 2013 pages 34-44 DOI:10.1080/17429145.2012.721523
Positive selection pressure on rice blast resistance allele Piz-t makes it divergent in Indian land races
Thakur et al.,
a National Research Centre on Plant Biotechnology , IARI , New Delhi , 110012 , India
b Deparment of Biotechnology , Himachal Pradesh University , Shimla , 171005 , India
... BioEdit Software version 7.0.9.0 (www.mbio.ncsu.edu). Gene coding regions were
predicted with FGENESH (www.softberry.com) using the Piz-t sequence as reference.
The functional domain(s) which play an important role ...
Scientia Horticulturae
Volume 164, 17 December 2013, Pages 323–332 DOI:10.1016/j.scienta.2013.09.040
Transcriptional profile of differentially expressed genes related to abortive flower buds under short light period stress in petunia
Yue et al.,
Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China
... 2.7. Sequence and bioinformatics analysis of Phms2. Through EST blast analysis in the
genome database of petunia, we successfully predicted the full-length open reading frame
(ORF) of Phms2 using the FGENESH tool (http://www.softberry.com). ...
Front Plant Sci.
2013; 4: 317. DOI:10.3389/fpls.2013.00317
In silico comparison of genomic regions containing genes coding for enzymes and transcription factors for the phenylpropanoid pathway in Phaseolus vulgaris L. and Glycine max L. Merr
Reinprecht et al.,
1Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
2Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
Edited by: Georgina Hernandez, Universidad Nacional Autonoma de Mexico, Mexico
Reviewed by: Alejandra A. Covarrubias, Universidad Nacional Autonoma de Mexico, Mexico; Steven B. Cannon, United States Department of Agriculture, USA
... The consensus sequence was analyzed for the presence of coding regions with GENSCAN
(http://genes.mit.edu/GENSCAN.html) and FGENESH (http://www.softberry.com/) using Medicago
truncatula and Arabidopsis, respectively as the model organisms. ...
ACS Chem. Biol.
2013, 8 (4), pp 741–748 DOI: 10.1021/cb3006787
Complexity Generation in Fungal Peptidyl Alkaloid Biosynthesis: A Two-Enzyme Pathway to the Hexacyclic MDR Export Pump Inhibitor Ardeemin
Stuart W. Haynes †, Xue Gao ‡, Yi Tang *‡§, and Christopher T. Walsh *†
† Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
‡Department of Chemical and Biomolecular Engineering and §Department of Chemistry and Biochemistry, University of California Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
... Contigs containing candidate clusters were examined using eukaryotic gene predictor
FGENESH (Softberry), and predicted proteins surrounding the candidate
Ant-activating NRPS were examined by repeated BLAST search. ...
Theoretical and Applied Genetics
Volume 126, Issue 7 , pp 1825-1838 DOI:10.1007/s00122-013-2095-8
Fine mapping and identification of candidate genes controlling the resistance to southern root-knot nematode in PI 96354
Anh-Tung Pham, Kaitlin McNally, Hussein Abdel-Haleem, H. Roger Boerma, Zenglu Li
1. Center for Applied Genetic Technologies and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
2. Institute for Plant Biology, University of Zurich, Zurich, Switzerland
3. Georgia Seed Development Commission, Athens, GA, 30605, USA
... genes. In addition to using soybase's gene model, we also used the programs
Fgenesh (http://linux1.softberry.com) and Expasy (http://web.expasy.org/cgi-bin/
translate/dna_aa) to predict gene structure and protein sequence. ...
Int. J. Mol. Sci.
2013, 14(7), 13559-13576; doi:10.3390/ijms140713559
First Insights into the Large Genome of Epimedium sagittatum (Sieb. et Zucc) Maxim, a Chinese Traditional Medicinal Plant
Liu et al.,
1 Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
2 University of Chinese Academy of Sciences, Beijing 100039, China
... protein database (NR) [72]. Secondly, ab initio gene prediction was performed on
the ENS dataset using the FGENESH feature (Dicot plants-Arabidopsis) of the
MolQuest software package (softberry) [73]. Thirdly, a local BLAST ...
J. Integr. Plant Biol.
(2013) 55(7):643–653. DOI:10.1111/jipb.12068
Genome-wide analysis of the Sus gene family in cotton.
Zou et al.,
State Key Laboratory of Cotton Biology, Institute of Cotton Research, the Chinese Academy of Agricultural Sciences, Anyang, China
... DNA sequences or were predicted online using FGENESH (http://linux1.softberry.com/berry.
phtml?topic=fgenesh&group=programs &subgroup=gfind). Predicted conserved domains
were screened by SMART (http://smart.embl-heidelberg.de/) and ...
Experimental & Molecular Medicine
(2013) 45, e31; doi:10.1038/emm.2013.59
A known expressed sequence tag, BM742401, is a potent lincRNA inhibiting cancer metastasis
Park et al.,
1Medical Genomics Research Center, KRIBB, Daejeon, Republic of Korea
2Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
3Department of General Surgery, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
... indicating that our putative lincRNAs are not protein-coding genes: first, when we predicted open
reading frames of our putative lincRNAs using gene prediction programs, such as GeneScan
(http://genes.mit.edu/GENSCAN.html) and FGENESH (http://www.softberry.com/), we ...
PloS one
February 01, 2013DOI: 10.1371/journal.pone.0055185
Genomic and Secretomic Analyses Reveal Unique Features of the Lignocellulolytic Enzyme System of Penicillium decumbens
Liu et al.,
State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China
Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
... Gene Finding and Annotation. Gene models were predicted independently with a set
of gene finders including Augustus [58], GeneMark-ES [59], GeneId [60] and SoftBerry
eukaryotic gene finding suite (Fgenesh and Fgenesh+) [61]. ...
Journal of Integrative Plant Biology
Volume DOI:10.1111/jipb.12150
Auxin biosynthesis by the YUCCA6 flavin monooxygenase gene in woodland strawberry (Fragaria vesca)
Liu et al.,
1Forestry and Fruit Tree Research Institute, Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai, China
2Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Biotechnology, SAAS, Shanghai, China
3Departamento de Biologia Moleculary Bioquimica, Universidad de Malaga, Malaga, Spain
... genes (Cheng et al. 2006) as query sequences. Hereafter, HMM-based gene structure
prediction was carried out using the FGENESH program (default values) at
http://linux1.softberry.com/berry.phtml. To confirm these candidates ...
BMC Genomics
2013, 14:60 doi:10.1186/1471-2164-14-60
Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements
Fellers et al.,
1 USDA-ARS, Hard Winter Wheat Genetics Research Unit, Department of Plant Pathology, Manhattan, KS, 66506, USA
2 Agriculture & Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, BC, V0H 1Z0, Canada
... Louis, MO. BAC clones were cultured, subcloned, shot gun sequenced, and assembled
(Washington University Genome Center, St. Louis, MO). Gene calls were made using FGENESH
with gene models specific to Puccinia (http://linux1.softberry.com/berry.phtml webcite;). ...
BMC plant biology
(2013). 13(1), 89. DOI:10.1186/1471-2229-13-89
Analysis of the WUSCHEL-RELATED HOMEOBOX gene family in the conifer picea abies reveals extensive conservation as well as dynamic patterns.
Hedman, H., Zhu, T., von Arnold, S., & Sohlberg, J. J.
Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO-Box 7080, Uppsala, SE, 75007, Sweden
... Gene predictions were performed with FGENESH (http://linux1.softberry.com/berry.phtml) trained
with dicot plants (Arabidopsis thaliana). Primer sequences are listed in Additional file 5. Gene and
cDNA accessions are listed in Additional file 6. Phylogenetic analysis ...
ChemBioChem.
(2013). Volume 15, Issue 2, pages 284–292, January 24, 2014 DOI:10.1002/cbic.201300626
Identification of the First Diphenyl Ether Gene Cluster for Pestheic Acid Biosynthesis in Plant Endophyte Pestalotiopsis fici
Xu et al.,
1State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101 (China)
2Beijing Institute of Pharmacology & Toxicology, 27 Taiping Road, Haidian District, Beijing 100850 (China)
... the accession number KC145148. The ORFs were predicted from the sequence by
using the GENSCAN Web Server at MIT (http://genes.mit.edu/GENSCAN.html) and
FGENESH (Softberry). The deduced proteins of corresponding ...
BMC plant biology
(2013). 13(1), 126. DOI:10.1186/1471-2229-13-126
Molecular cloning and characterisation of SlAGO family in tomato
Xian et al.,
Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 400044, People’s Republic of China
... After searching for AGO genes, bioinformatics tools, such as FGENESH (http://linux1.softberry.
com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind) was used to analyze and
predict those unknown SlAGOs, and BLASTX of NCBI (http://blast.ncbi.nlm.nih.gov/Blast ...
BMC genomics
(2013). 14(1), 1-11. DOI:
Haplotype analysis of sucrose synthase gene family in three Saccharum species
Zhang, J., Arro, J., Chen, Y., & Ming, R.
(1)College of Life Sciences, Fujian Normal University, Fuzhou, 350108, China
(2)Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
... For genomic sequences that had not previously been annotated, we supplemented the above methods with the
use of Genscan (http://?genes.?mit.?edu/?GENSCAN.?html)[43] and FGENESH (http://?linux1.?softberry.?com/?berry.?phtml) gene prediction software....
International journal of molecular sciences
(2013). 14(11), 22462-22482. DOI:10.3390/ijms141122462
Cloning, Characterization and Effect of TmPGRP-LE Gene Silencing on Survival of Tenebrio Molitor against Listeria monocytogenes Infection
Tindwa et al.,
1 Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Korea
2 National Research Laboratory of Defense Proteins, College of Pharmacy, Pusan National University, Jangjeon Dong, Kumjeong Ku, Busan 609-735, Korea
... 1.0, NetOGlyc, NetPhos 2.0 and NetPhosK 1.0 server respectively (Technical
University of Denmark, Lyngby, Denmark). The potential coding region was predicted
using FGENESH (Softberry, Inc., Mount Kisco, NY, USA) [44]. ...
BMC microbiology
(2013). 13(1), 165. DOI:10.1186/1471-2180-13-165
Conservation of the genes for HC-toxin biosynthesis in Alternaria jesenskae
Wight, W. D., Labuda, R., & Walton, J. D.
1 Department of Energy Plant Research Laboratory, Michigan State University, 612 Wilson Road, Room 210, East Lansing, MI 48824, USA
2 Romer Labs Division Holding GmbH, Technopark 1, Tulln 3430, Austria
... Page 14. (http://www.ebi.ac.uk/Tools/msa/clustalw2/), and SPIDEY (NCBI). Assembly of predicted
protein sequences was performed using DNASTAR Lasergene software with assistance from
FGENESH (www.softberry.com) with Alternaria as the training model. ...
BMC genomics
(2013). 14(1), 335. DOI:10.1186/1471-2164-14-335
Frequent loss of lineages and deficient duplications accounted for low copy number of disease resistance genes in Cucurbitaceae
Lin, X., Zhang, Y., Kuang, H., & Chen, J.
Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, P.R. China
... 3,110 protein sequences with ATP binding domain and 6,979 protein sequences with LRR domain
from NCBI was used to verify the potential NBS- LRR or LRR-LRK encoding genes [3]. All
identified sequences were annotated using FGENESH [www.softberry.com] and ...
BMC genomics
(2013). 14(1), 109. DOI:
Genome-wide analysis of NBS-encoding disease resistance genes in Cucumis sativus and phylogenetic study of NBS-encoding genes in Cucurbitaceae crops
Wan, H., Yuan, W., Bo, K., Shen, J., Pang, X., & Chen, J.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
...the upstream and downstream of BLAST hits, were annotated using the FGENESH...
PloS one
(2013). 8(4), e62288. DOI:10.1371/journal.pone.0062288
Genome-Wide Expression Analysis of Soybean MADS Genes Showing Potential Function in the Seed Development
Fan et al.,
MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, China
... The fragment genes were predicted the whole CDS by FGENESH (http://linux1.softberry.com/berry.phtml) or blasting the NCBI Ref-RNA database (Table S1)....
Mobile DNA
(2013). 4(1), 12.
Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements
Bao, W., & Jurka, J.
Genetic Information Research Institute, 1925 Landings Drive, Mountain View,
CA 94043, USA
... The TE-encoded multiple-exon genes were predicted by FGENESH program (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind), ...
BMC genomics
(2013). 14(1), 79. DOI:10.1186/1471-2164-14-79
Comparative genomics of Lupinus angustifolius gene-rich regions: BAC library exploration, genetic mapping and cytogenetics
Ksiazkiewicz et al.,
1 Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479, Poznan, Poland
2 Laboratory of Computational Genomics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland
...BAC sequences with masked repetitive regions were subjected to FGENESH [42,43]in silico gene prediction followed by BLAST against the EST, nr, and Swiss-Prot [44] c...
Nature Genetics
2012 44, 1060–1065. doi:10.1038/ng.2372
Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses.
O'Connell et al.,
Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
Centro Hispano-Luso de Investigaciones Agrarias, Departamento de Microbiologia y Genetica, Universidad de Salamanca, Villamayor, Spain.
...Gene structures were predicted using the Broad Institute automated gene-calling pipeline35
based on a combination of gene models predicted by the programs FGENESH (Softberry Inc., USA),
GENEID36, GeneMark37, SNAP38 and Augustus39 together with EST-based and manually curated gene models.
GENEID, FGENESH, SNAP and Augustus were trained using a set of high-confidence EST-based gene models
generated by clustering Blat-aligned species-specific ESTs....
J. Exp. Bot.
(2012) 63 (1): 203-214. doi: 10.1093/jxb/err264
Molecular characterization of 60 isolated wheat MYB genes and analysis of their expression during abiotic stress
Lichao Zhang,
Guangyao Zhao,
Jizeng Jia,
Xu Liu and
Xiuying Kong *
The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
... Only the sequences that shared >95% matches were considered redundant. The
open reading frames (ORFs) were predicted using FGENESH (http://www.softberry.com) and were translated into amino acid sequences. Finally ...
Applied Microbiology and Biotechnology
June 2012 DOI
10.1007/s00253-012-4130-0
Identification of a brevianamide F reverse prenyltransferase BrePT from Aspergillus versicolor with a broad substrate specificity towards tryptophan-containing cyclic dipeptides
Suqin Yin,
Xia Yu,
Qing Wang,
Xiao-Qing Liu,
Shu-Ming Li
1. College of Life Sciences, Capital Normal University, No.105 Xisanhuan Beilu, Beijing, 100048, China
2. Institut fur Pharmazeutische Biologie und Biotechnologie, Philipps-Universitat Marburg, Deutschhausstrasse 17A, 35037, Marburg, Germany
... Computer-assisted sequence analysis FGENESH (Softberry, Inc.) and the DNASIS
software pack- age (version 2.1: Hitachi Software Engineering, San Bruno, CA) were
used for intron prediction and sequence analysis, respectively. ...
Journal of Industrial Microbiology & Biotechnology
June 2012, Volume 39, Issue 6, pp 869-876 DOI: 10.1007/s10295-012-1087-z
High-level expression of a novel Penicillium endo-1,3(4)-b-d-glucanase with high specific activity in Pichia pastoris
Chen et al.,
1. Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People’s Republic of China
... respectively. The cod- ing region was predicted online using the FGENESH program
(http://linux1.softberry.com/berry.phtml/). SignalP 4.0 web server (http://www.cbs.dtu.
dk/services/SignalP/) was used to predict the signal peptide. ...
Immunogenetics
DOI: 10.1007/s00251-012-0672-7
Immunoglobulin genes of the turtles
Susana Magadan-Mompo, Christian Sanchez-Espinel &
Francisco Gambon-Deza
Servicio Gallego de Salud (SERGAS) Unidad de Inmunologia,
Hospital do Meixoeiro, Carretera de Madrid s/n,
Vigo 36210, Pontevedra, Spain
Shared Unit of Immunology, Vigo University Hospital Complex
(Hospital Meixoeiro), University of Vigo,
Edificio de Ciencias Experimentales, Rua das Abeleiras,
Campus As Lagoas-Marcosende,
Vigo 36310, Pontevedra, Spain
... Identification
of the exons coding for the constant heavy (CH) domains was performed using the software
FGENESH (www.softberry.com) (Solovyev et al. 2006; Yao et al. ...
Advances in Environment, Computational Chemistry and Bioscience
ISBN: 978-1-61804-147-0
In silico study of non-coding, coding transcription region and domain
interaction for chromosomal translocation sequences
PRAVEEN KUNAR KORLA 1, SHAN-CHIH LEE 2 , JIM SHEU 3, JACK CHENG 3,
KA-LOK NG 1
1 Department of Biomedical Informatics,Asia University, Taichung,TAIWAN 41354
2 School of Medical Imaging and Radiological Sciences, Chung Shan Medical University, Taichung, TAIWAN
40201
... The URL addresses for these web based tools are;Fgenesh (http://linux1.softberry.com/berry.
phtml), Genemark (http://exon.gatech.edu/eukhmm.cgi), Genscan (http://immunax.dfci.harvard.
edu/Tools/genscan.ht ml) and Webgene (http://zeus2.itb.cnr.it/~webgene/genebuilder.html ...
Cereal Research Communications
Volume 40, Number 3/September 2012 pp. 362-372 DOI: 10.1556/CRC.40.2012.3.5
Molecular mapping of quantitative trait loci for flag leaf length and other agronomic traits in rice (Oryza sativa)
Sonah et al.,
1 National Research Centre on Plant Biotechnology New Delhi 110012 India
2 Directorate of Rice Research Hyderabad AP India
... sativa subsp. japonica cv. Nipponbare (http://rice.plantbiology.msu.edu/) was used
for gene prediction. FGENESH gene prediction software (www.softberry.com) was
used to predict genes in this sequence. Predicted genes ...
Animal Science Journal
Volume 83, Issue 5, pages 386–393, May 2012 DOI: 10.1111/j.1740-0929.2011.00975.x
Predictive mutational bioinformatic analysis of variation in the skin and wool associated corneodesmosin (CDSN) gene in sheep
SUBRAMANIAM et al.,
1 Western Australian Biomedical Research Institute (WABRI) & Centre for Health Innovation Research Institute (CHIRI), School of Biomedical Sciences, Curtin University, Perth
2 School of Biological Sciences, Murdoch University, Murdoch, Australia
... Gene prediction tools such as GENSCAN (Burge & Karlin 1997), FGENESH
(http://www.softberry.com), HMM gene (http://www.cbs.dtu.dk/services/HMMgene/),
Augus- tas (Stanke et al. 2006) and GeneMark (Lomsadze et al. ...
Mol Biol Evol
(2012) 29 (2): 861-871.
doi: 10.1093/molbev/msr261
First published online: October 14, 2011
Dynamic Gene Copy Number Variation in Collinear Regions of Grass Genomes
Jian-Hong Xu 1,†, Jeffrey L. Bennetzen 2 and Joachim Messing 1
1 Waksman Institute of Microbiology, Rutgers, The State University of New Jersey
2 Department of Genetics, University of Georgia
... About 100 kb–1 Mb chromosomal regions of alpha setarin gene loci were annotated by
Fgenesh software (http://linux1.softberry.com/berry.phtml) for gene models, and repeats
sequences were masked by Repeatmasker (http://www.repeatmasker.org/). ...
Archives of Insect Biochemistry and Physiology
Volume 79, Issue 2, pages 87–103, February 2012 DOI: 10.1002/arch.21014
ANNOTATION AND EVOLUTION OF THE ANTIOXIDANT GENES IN THE SILKWORM, Bombyx mori
Gui-Qin Shi 1, Quan-You Yu 1, Ze Zhang 1,2
1The Institute of Agricultural and Life Sciences, Chongqing University, Chongqing, China
2The Key Sericultural Laboratory of the Agricultural Ministry of China, Southwest University, Chongqing, China
... If some genome sequences showed even weak sequence similarity to any query sequences,
their flanking regions (1 kb or more long) were manually extracted, and then put them into
Softberry database to predict new genes using FGENESH program. ...
Journal of Microbiological Methods
Volume 91, Issue 3, December 2012, Pages 412–419 DOI: 10.1016/j.mimet.2012.09.014
Rapid screening of an ordered fosmid library to clone multiple polyketide synthase genes of the phytopathogenic fungus Cladosporium phlei
Kum-Kang So et al.,
a Institute for Molecular Biology and Genetics, Chonbuk National University, Jeonju, Chonbuk 561-756, Republic of Korea
b Department of Bio-Environmental Chemistry, Wonkwang University, Iksan, Chonbuk 570-749, Republic of Korea
... The structures of putative PKS genes and proteins were determined using FGENESH
(http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind)
and INTERPROSCAN (http://www.ebi.ac.uk/Tools/pfa/iprscan/), respectively. ...
Fungal Genetics and Biology
Volume 49, Issue 12, December 2012, Pages 977–986 DOI: 10.1016/j.fgb.2012.08.008
Reproductive mode and life cycle of the ash dieback pathogen Hymenoscyphus pseudoalbidus
A. Gross a, P.L. Zaffarano a, A. Duo a, C.R. Grunig b,
a Forest Pathology and Dendrology, Institute of Integrative Biology (IBZ), ETH Zurich, Universitatsstrasse 16, 8092 Zurich, Switzerland
b Microsynth AG, Schutzenstrasse 15, 9436 Balgach, Switzerland
... Initial sequence analysis was conducted with the basic local alignment search tool (BLAST,
http://blast.ncbi.nlm.nih.gov/Blast.cgi) and refined by the gene structure prediction program
FGENESH (http://linux1.softberry.com/berry.phtml) using the matrices of Sclerotinia ...
Applied Microbiology and Biotechnology
August 2012, Volume 95, Issue 4, pp 947-955 DOI: 10.1007/s00253-011-3807-0
A novel thermoacidophilic and thermostable endo-b-1,4-glucanase from Phialophora sp. G5: its thermostability influenced by a distinct b-sheet and the carbohydrate-binding module
Zhao et al.,
1. Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People’s Republic of China
... ncbi.nlm.nih.gov/BLAST/), respectively. Introns, exons, and transcription initiation sites were
predicted using the online software FGENESH (http://linux1.softberry.com/berry.phtml). The signal
peptide was predicted using SignalP (http://www. cbs.dtu.dk/services/SignalP/). ...
The FASEB Journal
Published online before print September 20, 2012 DOI: 10.1096/fj.12-219444
Regulation of Anopheles gambiae male accessory gland genes influences postmating response in female
Dottorini et al.,
*Department of Experimental Medicine and
†Department of Industrial Engineering, University of Perugia, Perugia, Italy;
‡Department of Biological Sciences, Imperial College London, South Kensington Campus, London, UK;
... The full-length sequence, structure, and the multiple variants of the HSF gene were predicted
using FGENESH-C, FGENESH (http://linux1.softberry.com/), Wise2 (http:// www.ebi.ac.uk/), and
Genescan (http://genes.mit.edu/ GENSCAN.html). Mosquito rearing and mating analysis ...
Journal of Zhejiang University SCIENCE B
June 2012, Volume 13, Issue 6, pp 452-464 DOI: 10.1631/jzus.B1100338
Genomic organization and sequence dynamics of the AvrPiz-t locus in Magnaporthe oryzae
Ping Li, Bin Bai, Hong-yan Zhang, Heng Zhou, Bo Zhou
1. State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
2. Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
... The Page 3. Li et al. / J Zhejiang Univ-Sci B (Biomed & Biotechnol) 2012 13(6):452-464 454 BAC
sequence was annotated by using gene predic- tion program and homology search. The Fgenesh
program (http://www.softberry.com) was used for gene prediction. ...
Journal of Bioscience and Bioengineering
Volume 113, Issue 6, June 2012, Pages 710–714 DOI: 10.1016/j.jbiosc.2012.02.005,
Cloning, over-expression and characterization of an alkali-tolerant endo-b-1,4-mannanase from Penicillium freii F63
Wang et al.,
1 Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
2 Engineering Research Centre for the Protection and Utilization of Bioresource in Southern China, College of Life Science, South-Central University for Nationalities, Wuhan 430074, PR China
... The online software FGENESH (http://linux1.softberry.com/berry.phtml) was used to predict
introns, exons and transcription initiation sites of the DNA sequence. The signal peptide was
predicted using SignalP (http://www.cbs.dtu.dk/services/SignalP/). ...
New Phytologist
Volume 193, Issue 4, pages 1049–1063, March 2012 DOI: 10.1111/j.1469-8137.2011.04006.x
Tracing the origin and evolutionary history of plant nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes
Jia-Xing Yue 1,2, Blake C. Meyers 3, Jian-Qun Chen 1, Dacheng Tian 1, Sihai Yang 1
1 State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
2 Department of Ecology and Evolutionary Biology, Rice University, Houston, TX 77005, USA
... In addition, the nucleotide sequences of these two genes, together with their 5? and 3? flanking
regions (each 5000 bp, respectively), were used for re-annotation with FGENESH
(http://linux1.softberry.com/berry.phtml) and the domain architecture of the resulting predicted ...
PLoS ONE 7
(7): e40564. doi:10.1371/journal.pone.0040564
Identification of a Polyketide Synthase Required for Alternariol (AOH) and Alternariol-9-Methyl Ether (AME) Formation in Alternaria alternata
Saha et al.,
Department of Microbiology, Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
Department of Food Chemistry, Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
... A. alternata. Intron-exon borders were predicted using FGENESH (softberry.com)
trained on A. brassicicola gene models but have not yet been verified experimentally
due to the rather large nature of PKS genes. Among these ...
Gene
Volume 500, Issue 1, 25 May 2012, Pages 73–79 DOI: 10.1016/j.gene.2012.02.051
Two novel N-terminal coding exons of Prkar1b gene of mouse: Identified using a novel approach of in silico and molecular biology techniques
Abdul Rouf Banday, Shafquat Azim, Sayeed Ur Rehman, Mohammad Tabish
Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
... and Borodovsky, 1998) and is available at http://www.cbs.dtu.dk/services/HMMgene, Genescan
(http://genes.mit.edu/GENSCAN.html), GeneSplicer available at http://cbcb.umd.edu/software/
GeneSplicer/ (Pertea et al., 2001), and FGENESH (http://www.softberry.com/berry.phtml ...
Developmental & Comparative Immunology
Volume 38, Issue 1, September 2012, Pages 1–9 DOI: 10.1016/j.dci.2012.03.001
Snakes antibodies
Francisco Gambon-Deza a, Christian Sanchez-Espinel b, Serafin Mirete-Bachiller a, Susana Magadan-Mompo c
a Servicio Gallego de Salud (SERGAS) Unidad de Inmunologia, Hospital do Meixoeiro, Carretera de Madrid s/n, Vigo 36210, Pontevedra, Spain
b Shared Unit of Immunology, University of Vigo – Vigo University Hospital Complex (Hospital Meixoeiro), Edificio de Ciencias Experimentales, Rua das Abeleiras, Campus As Lagoas-Marcosende, Vigo 36310, Pontevedra, Spain
... previously published reptile immunoglobulin mRNAs. Limits were deduced following
instructions in the software FGENESH (http://www.softberry.com) and Augustus
(http://www.augustus.gobics.de/submission). In Additional File A ...
Bioresource Technology
Volume 130, February 2013, Pages 161–167 DOI: 10.1016/j.biortech.2012.12.067
Characterization of three novel thermophilic xylanases from Humicola insolens Y1 with application potentials in the brewing industry
Yanlong Du et al.,
a Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
b College of Biological Science and Engineering, Bei Fang University of Nationalities, Yinchuan 750021, PR China
... The sequence assembly was performed using the Vector NTI Advance 10.0 software
(Invitrogen). Genes, introns, exons and transcription initiation sites were predicted using
the online software FGENESH (http://linux1.softberry.com/berry.phtml). ...
Molecular Plant Pathology
Volume 13, Issue 9, pages 1089–1100, December 2012 DOI: 10.1111/j.1364-3703.2012.00818.x
Degradation of aromatic compounds through the b-ketoadipate pathway is required for pathogenicity of the tomato wilt pathogen Fusarium oxysporum f. sp. lycopersici
Caroline B. Michielse 1,†,*, Linda Reijnen 1,‡, Chantal Olivain 2, Claude Alabouvette 2, Martijn Rep 1
1Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
2UMR 1229 INRA, Universite de Bourgogne Microbiologie du Sol et de l'Environnement, Dijon, France
... 1996). The annotated FOXG_17757 gene lacks a 5' and 3' end. In this article, we
suggest a new gene model based on fgenesh and augustus gene prediction software
(http://www.softberry.com, http://augustus.gobics.de/). This ...
Theoretical and Applied Genetics
May 2012, Volume 124, Issue 7, pp 1173-1182 DOI: 10.1007/s00122-011-1777-3
Localization of high level of sequence conservation and divergence regions in cotton
Wang et al.,
1. National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
... hmm (Brudno et al. 2003), GENSCAN (Lomsadze et al. 2005) and FGENESH
(http://linux1.soft- berry.com). The predicted genes were confirmed using BLASTN
queries against the cotton EST database. To annotate genes, predicted ...
Genes & genomics
2012, vol. 34, no4, pp. 379-390
The NPR1 family of transcription cofactors in papaya: insights into its structure, phylogeny and expression
Santy et al.,
(1) Unidad de Biotecnologia, Centro de Investigacion Cientifica de Yucatan (CICY), C. 43, No. 130, Col. Chuburna de Hidalgo, Merida, Yucatan, Mexico
... Page 3. Genes & Genomics 1997). The open reading frames (ORFs) in the papaya DNA contigs
harboring NPR1 homologues were predicted by the FGENESH program with the A. thaliana
genome set as refer- ence (http://linux1.softberry.com/berry.phtml). ...
Applied Microbiology and Biotechnology
November 2012, Volume 96, Issue 4, pp 951-962 DOI: 10.1007/s00253-012-3873-y
Expression and characterization of a novel metagenome-derived cellulase Exo2b and its application to improve cellulase activity in Trichoderma reesei
Geng et al.,
1. Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China
2. Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
... The resulting reads were assembled using Newbler version 2.0 (http://www.454.com). ORFs
in the assembled sequences were predicted by FGENESB (Softberry, Goteborg, Sweden) and
a BLASTX search performed against the NR database to access annotation information. ...
ChemBioChem
Volume 13, Issue 17, pages 2583–2592, November 26, 2012 DOI: 10.1002/cbic.201200523
Identification of the Verruculogen Prenyltransferase FtmPT3 by a Combination of Chemical, Bioinformatic and Biochemical Approaches
Kathrin Mundt 1, Beate Wollinsky 1, Prof. Dr. Han-Li Ruan 2, Assoc. Prof. Dr. Tianjiao Zhu 3, Prof. Dr. Shu-Ming Li1
1Philipps-Universitat Marburg, Institut fur Pharmazeutische Biologie und Biotechnologie, Deutschhausstrasse 17A, 35037 Marburg (Germany)
2Huazhong University of Science and Technology, Faculty of Pharmacy, Tongji Medical College and Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Hongkong Road 13, 430030, Wuhan (China)
... Computer-assisted sequence analysis: The DNASIS software package (version 2.1; Hitachi
Software Engineering, San Bruno, CA) and FGENESH (Softberry, Inc.; http://www.softberry.com/
berry.phtml) were used for intron prediction and sequence analysis, respectively. ...
Molecular Genetics and Genomics
May 2012, Volume 287, Issue 5, pp 373-388 DOI: 10.1007/s00438-012-0682-z
Comparative mapping, genomic structure, and expression analysis of eight pseudo-response regulator genes in Brassica rapa
Jin A. Kim et al.,
1. Department of Agricultural Bio-resources, National Academy of Agricultural Science, Rural Development Administration, 224 Suinro Gwonseon-gu, Suwon, Gyeonggi-do, 441-707, Republic of Korea
2. National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Republic of Korea
... gov/BLAST/) were used when needed. Gene annotation was achieved using the
Web-based gene-prediction program FGENESH Arabid- opsis (http://www.softberry.
com/berry.phtml). A phylogenetic tree was constructed using ...
FEBS Journal
Volume 279, Issue 4, pages 572–585, February 2012 DOI: 10.1111/j.1742-4658.2011.08446.x
Identification and expression analysis of three novel splice variants of protein kinase A catalytic b subunit gene in the mouse using combinatorial in silico and molecular biology approaches
Abdul R. Banday, Shafquat Azim, Mohammad Tabish
Department of Biochemistry, Faculty of Life Sciences, AM University, Aligarh, India
... The FGENESH tool (http://www.softberry.ru/berry.phtml) was used for defining the
structural features of gene under study. The ... sequence motifs/rules [53,54]. FEX tool
(http://www.softberry.ru/berry.phtml) was used for validation of new ...
Theoretical and Applied Genetics
August 2012, Volume 125, Issue 4, pp 715-729 DOI: 10.1007/s00122-012-1863-1
Identification of FAD2 and FAD3 genes in Brassica napus genome and development of allele-specific markers for high oleic and low linolenic acid contents
Qingyong Yang et al.,
1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
... The nonredundant sequences resulted from the hits were then collected and compared with known
FAD2 and FAD3 genes in Arabidopsis . The program FGENESH (HMM-based gene structure
prediction tool) was used for gene prediction (http:// www.softberry.com/). ...
Molecular Biology Reports
April 2012, Volume 39, Issue 4, pp 3375-3383 DOI: 10.1007/s11033-011-1108-4
Differentially expressed three non-coding alternate exons at 5? UTR of regulatory type I beta subunit gene of mouse
Abdul Rouf Banday, Shafquat Azim, Mohammad Tabish
1. Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, UP, 202002, India
... Gene/ Exon finding tools were used at HMMgene (http://www.cbs. dtu.dk/services/HMMgene),
Genescan (http://genes.mit.edu/ GENSCAN.html), GeneSplicer (http://cbcb.umd.edu/software/
GeneSplicer/), FGENESH (http://www.softberry.com/berry. phtml). ...
Canadian Journal of Microbiology
2012, 58(7): 815-827, DOI: 10.1139/w2012-054
Gene cloning, molecular modeling, and phylogenetics of serine protease P32 and serine carboxypeptidase SCP1 from nematophagous fungi Pochonia rubescens and Pochonia chlamydosporia
Eduardo Larriba, a,c Jose Martin-Nieto, b,c Luis Vicente Lopez-Llorca a,c
aDepartment of Marine Sciences and Applied Biology, University of Alicante, P.O. Box 99, E-03080 Alicante, Spain.
bDepartment of Physiology, Genetics and Microbiology, University of Alicante, P.O. Box 99, E-03080 Alicante, Spain.
... lyon1.fr/cap3.php. Gene prediction was made using FGENESH/HMM based on
Neurospora genes (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=
programs&subgroup =gfind). Pairwise alignments were carried ...
PNAS
August 7, 2012 vol. 109 no. 32 E2155-E2164 DOI: 10.1073/pnas.1117982109
Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering
Zhengjun Xia et al.,
aNortheast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China;
bSoybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan;
... 2 B and C). A single intron-free gene (AB552962, 525 bp, 174 aa) was consistently identified
by GenScan (45), GeneMark (46), FGENESH (http://linux1.softberry.com/berry.phtml), and
RiceGAAS (44) for the dominant E1 genotype (Misuzudaizu and Harosoy-E1), and was ...
Comparative and Functional Genomics
Volume 2012 (2012), Article ID 914843, 14 pages
doi:10.1155/2012/914843
In Silico Identification and Comparative Genomics of Candidate Genes Involved in Biosynthesis and Accumulation of Seed Oil in Plants
Arti Sharma and Rajinder Singh Chauhan
Department of Biotechnology & Bioinformatics, Jaypee University of Information Technology, Waknaghat, P.O. Dumehar Bani, Kandaghat, Solan 173 215, India
... Rapa, and soybean sequences were further annotated for gene models (open reading frames,
including the 5?UTRs and 3?UTRs) using gene prediction algorithms of FGenesH
(http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind) [43– ...
Genetics
August 17, 2012 genetics.112.144436 DOI:10.1534/genetics.112.144436
High Throughput Discovery of Mutations in tef Semi-dwarfing Genes by Next Generation Sequencing Analysis
Qihui Zhu et al.,
1 University of Georgia;
2 Purdue University
... The complete clone sequences were submitted to GenBank (Accession numbers:
JN672669-JN672670). The fosmid sequences were initially annotated by FGENESH
(http://www.softberry.com) and GENESCAN (Buger and Karlin 1997). Putative proteins ...
Theoretical and Applied Genetics
November 2012, Volume 125, Issue 7, pp 1525-1537 DOI: 10.1007/s00122-012-1931-6
Development of candidate gene markers associated to common bacterial blight resistance in common bean
Chun Shi et al.,
1. Greenhouse and Processing Crops Research Centre, Agriculture and Agri-Food Canada, Harrow, ON, N0R 1G0, Canada
2. Department of Plant Agriculture, University of Guelph, Crop Science Building, Guelph, ON, N1G 2W1, Canada
... for Bio- technology Information (NCBI) database. Gene predictions were based on
ab initio method by FGENESH software using Medicago gene model (http://www.
softberry.com). Sequences were subjected to BlastN similarity ...
Mol Genet Genomics.
2012 Oct;287(10):765-84. Epub 2012 Aug 24.
Auxin response factor gene family in Brassica rapa: genomic organization, divergence, expression, and evolution
Mun JH et al.,
Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
... Since the draft B. rapa genome did not provide information on the 50- and 30-UTR
regions of the gene models, we used in-house trained FGENESH (www.
softberry.com) to predict the 50- and 30-UTR regions of the BrARF genes. ...
PLoS ONE
7(9): e45307. doi:10.1371/journal.pone.0045307
Genome Dynamics Explain the Evolution of Flowering Time CCT Domain Gene
Families in the Poaceae.
Cockram et al.,
1 John Bingham Laboratory, National Institute of Agricultural Botany, Huntington Road, Cambridge, United Kingdom, 2 Leibniz Institute for Plant Genetics and Crop Plant
Research (IPK), Gatersleben, Germany, 3 Leibniz Institute for Age Research, Fritz Lipmann Institute (FLI), Jena, Germany, 4 Department of Computational and Systems
Biology, John Innes Centre, Norwich, United Kingdom
... helmholtz-muenchen.de/plant/triticeae/) or fl-cDNAs [40]. De novo gene predictions
and reassessments were conducted using FGENESH (http://www.softberry.com/)
using 'monocot' as the basis of gene prediction. Homology ...
PLoS ONE
7(9): e45307. doi:10.1371/journal.pone.0045307
Genome Dynamics Explain the Evolution of Flowering Time CCT Domain Gene Families in the Poaceae
Cockram et al.,
John Bingham Laboratory, National Institute of Agricultural Botany, Huntington Road, Cambridge, United Kingdom
Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
...De novo gene predictions and reassessments were conducted using FGENESH (http://www.softberry.com/) using ‘monocot’ as the basis of gene prediction. ...
African Journal of Biotechnology
Vol. 11(77), pp. 14123-14131, 25 September, 2012
DOI: 10.5897/AJB12.778
Molecular cloning and characterization of an acyl-ACP thioesterase gene (AhFatB1) from allotetraploid peanut (Arachis hypogaea L.)
Wen Qigen, Lei Yong, Huang Jiaquan, Jiang Huifang and Liao Boshou
Oil Crop Research, Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, P. R. China.
... The theoretical molecular weight and isoelectric point of deduced polypeptide were predicted
using the ProtParam program (http://www.expasy.ch/tools/protparam.html), and Exon-Intron
analysis was made with the FGENESH program (http://linux1.softberry.com/). ...
Molecular Genetics and Genomics
March 2012, Volume 287, Issue 3 , pp 189-203 DOI: 10.1007/s00438-011-0671-7
Transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes provides insight into LeMADS-RIN-regulated ethylene-dependent as well as ethylene-independent aspects of ripening in tomato
Rahul Kumar, Manoj K. Sharma, Sanjay Kapoor, Akhilesh K. Tyagi, Arun K. Sharma
1. Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
2. Department of Plant Pathology, University of California, Davis, CA, 95616, USA
... Gene structure of these BAC sequences was predicted using FGENESH (http://linux1.
softberry.com/berry.phtml?topic=fgenesh& group=programs&subgroup=gfind) and 2 kb
sequences upstream to predicted open reading frames were extrac- ted. ...
Molecular Biology Reports
Volume 40, Issue 2 , pp 1385-1396 DOI: 10.1007/s11033-012-2182-y
Characterization of the NADP-malic enzymes in the woody plant Populus trichocarpa
Yu et al.,
1. State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
... We performed the PtNADP-ME4 gene structure (exons and introns) prediction using the
FGENESH program on the SoftBerry server (http://www.soflberry.corn/berry.phtml), and
present new predicted PtNADP-ME4 gene sequences (Table S1). ...
Plant Disease
February 2013, Volume 97, Number 2
Pages 245-251
http://dx.doi.org/10.1094/PDIS-11-11-0941-RE
Chromosomal Mapping and QTL Analysis of Resistance to Downy Mildew in Cucumis sativus
Zhang et al.,
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
College of Agriculture, Guizhou University, Guiyang 550025, China
... Only matches with an identity of ? 95% were retained. Gene prediction was performed with the
computer program BGF (http://bgf.genomics.org.cn) and veriWed by FGENESH (http://sunl.softberry.
com/) (40), GENESCAN (http://genes.mit.edu/GENSCAN.html) (4), TwinScan ...
PLoS ONE
7(12): e53401. doi:10.1371/journal.pone.0053401
A Novel Family of Terminal-Repeat Retrotransposon in Miniature (TRIM) in the Genome of the Red Harvester Ant, Pogonomyrmex barbatus
Yihong Zhou, Sara Helms Cahan
Department of Biology, University of Vermont, Burlington, Vermont, United States of America
... assembly. Elements along with their flanking sequences were submitted to FGENESH
program (Softberry, Inc., http://linux1.softberry.com/berry.phtml?topic=
fgenesh&group=programs&subgroup=gfind) for gene prediction. ...
J Hered
(2012) doi: 10.1093/jhered/ess102
Identification and Characterization of a Homologue to the Arabidopsis INDEHISCENT Gene in Common Bean
Gioia T, Logozzo G, Kami J, Zeuli PS, Gepts P.
From the Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Universita degli Studi della Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy (Gioia, Logozzo, Spagnoletti Zeuli); and the Department of Plant Sciences/MS1, University of California, 1 Shields Avenue, Davis, CA 95616–8780 (Kami and Gepts).
... with AtIND. Gene structure was predicted using the software FGENESH
(http://linux1.softberry.com/berry.phtml), whereas the search for ORFs was performed
using ORF finder (http://www.ncbi.nlm.nih.gov/projects/gorf/). To identify ...
Theoretical and Applied Genetics
Volume 125, Issue 2 , pp 223-234 DOI: 10.1007/s00122-012-1827-5
Map-based cloning of a recessive genic male sterility locus in Brassica napus L. and development of its functional marker
Li et al.,
1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
2. Institute of Industrial Crops, Henan Academy of Agricultural Science, Zhengzhou, 450002, China
... Gene prediction and plant transformation The website-based software FGENESH (http://www.soft
berry.com) was applied to predict the putative ORF from the candidate region. The genomic or
coding sequences of predicted genes were submitted to NCBI (http://www.ncbi. ...
New Phytologist
Volume 197, Issue 2, pages 416–430, January 2013 DOI: 10.1111/nph.12026
Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body DNA methylation in open chromatin state
Lafon-Placette et al.,
1Universite d'Orleans, Faculte des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Orleans, France
2INRA, USC1328 Arbres et Reponses aux Contraintes Hydriques et Environnementales (ARCHE), Orleans, France
... Identification of transposase was performed using Fgenesh software (http://linux1.softberry.com/
berry.phtml?topic=fgenesh&group=programs&subgroup=gfind) and confirmed by TBlastX
analysis (e-value < 10 ?30 ) on a flowering plant transcripts database. ...
BMC Genomics
2012, 13:409
http://www.biomedcentral.com/1471-2164/13/409
Evolution of the Rdr1 TNL-cluster in roses and
other Rosaceous species
Diro Terefe-Ayana, Helgard Kaufmann, Marcus Linde and Thomas Debener
Institute for Plant Genetics, Leibniz University Hannover, Herrenhaeuser Str. 2,
Hannover 30419, Germany
... Gene prediction and annotation based on the completely assembled sequence was carried out using the gene prediction program
FGENESH (http://www.softberry.com). ...
Journal of Plant Interactions
Volume 8, Issue 1, 2013 pages 34-44 DOI: 10.1080/17429145.2012.721523
Positive selection pressure on rice blast resistance allele Piz-t makes it divergent in Indian land races
Thakur et al.,
a National Research Centre on Plant Biotechnology, IARI, New Delhi, 110012, India
b Deparment of Biotechnology, Himachal Pradesh University, Shimla, 171005, India
... [CrossRef], [PubMed], [Web of Science ®], [CSA] View all references) and manually edited using
BioEdit Software version 7.0.9.0 (www.mbio.ncsu.edu). Gene coding regions were predicted
with FGENESH (www.softberry.com) using the Piz-t sequence as reference. ...
Mycology: An International Journal on Fungal Biology
Volume 3, Issue 1, 2012 pages 54-64 DOI: 10.1080/21501203.2011.654353
Two arginine biosynthesis genes are essential for pathogenicity of Colletotrichum higginsianum on Arabidopsis
Hiroyuki Takahara ab*, Aurelie Huser b & Richard O'Connell b
a Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
b Max Planck Institute for Plant Breeding Research, Department of Plant–Microbe Interactions, Cologne, Germany
... 2007) and the FGENESH prediction tool using Fusarium and Magnaporthe matrices (Softberry
Inc., Mount Kisco, NY, USA). Sequence homology searches were performed against the
NCBI nr protein data base using appropriate BLAST algorithms. ...
PLoS ONE
7(9): e44264. doi:10.1371/journal.pone.0044264
Identification and Sequence Analysis of Metazoan tRNA 3?-End Processing Enzymes tRNase Zs.
Wang et al.,
Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
... The splicing pattern was verified using the Fgenesh and Fgenesh_GC programs provided at the Softberry website (http://linux1.softberry.com/berry.phtml??topic=fgenesh). ...
Theoretical and Applied Genetics
Volume 125, Issue 2 , pp 211-222 DOI: 10.1007/s00122-012-1826-6
Exploiting comparative mapping among Brassica species to accelerate the physical delimitation of a genic male-sterile locus (BnRf) in Brassica napus
Yanzhou Xie et al.,
1. National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement (Wuhan Branch), Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China
2. College of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, People’s Republic of China
... Biosystems, Foster City, CA, USA). Software packages FGENESH (http://www.softberry.
com) and Glim- merHMM (Majoros et al. 2004) were both applied to pre- dict the putative
ORF from the candidate region. The genomic or coding ...
Planta
Volume 237, Issue 1 , pp 279-292 DOI: 10.1007/s00425-012-1756-1
Young Leaf Chlorosis 1, a chloroplast-localized gene required for chlorophyll and lutein accumulation during early leaf development in rice
Kunneng Zhou et al.,
1. National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
2. National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
... P0027G10. Within this region, five ORFs were predicted using the program FGENESH
2.2 (http://www. softberry.com) (Fig. 2b). To determine the mutation site, all five cDNA
sequences were separately isolated from young leaves. ...
PLoS ONE
7(12): e52293. doi:10.1371/journal.pone.0052293
Full-Length Minor Ampullate Spidroin Gene Sequence.
Chen et al.,
Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, People's Republic of China
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
... Fgenesh 2.6 (http://linux1.softberry.com/berry.phtml??topic=fgenesh&group=programs&subgroup=gf?ind) was used for intron prediction. ...
BMC Plant Biology
2012, 12:85 DOI: 10.1186/1471-2229-12-85
Analyses of the sucrose synthase gene family in cotton: structure, phylogeny and expression patterns
Chen et al.,
1 School of Agriculture and Food Science, Zhejiang A & F University, Lin'an, Hangzhou, Zhejiang 311300, China
2 State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
... As the absence of the cDNA sequence, the exon/intron structure of GaSus2 was predicted online
using the FGENESH algorithm (http://linux1.softberry.com/berry.phtml), which resulted in the
definition of 10 putative introns within its putative coding regions. ...
Genomics
Volume 99, Issue 4, April 2012, Pages 241–245 DOI:10.1016/j.ygeno.2012.01.007
Evolutionary genomics reveals the premetazoan origin of opposite gating polarity in animal-type voltage-gated ion channels
Xinjiang Cai
Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
Department of Molecular Pathogenesis, New York University Langone Medical Center, New York, NY 10016, USA
... In cases when TBlastN searches identified putative genes of interest that had not been annotated,
or when currently annotated genes in the databases were believed to be incomplete,
GeneMark.hmm and FGENESH programs (http://www.softberry.com/berry.phtml?topic ...
BMC Genomics
2012, 13:253 doi:10.1186/1471-2164-13-253
Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa)
Chai et al.,
1 Key Laboratory of Biofuels, Chinese Academy of Sciences, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
2 Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
... Subsequently, manual reannotation was performed to correct the putative CCCH sequences
using online web server FGENESH (http://linux1.softberry.com/berry.phtml webcite). In this
endeavor, 12 protein sequences were corrected for further analysis. ...
ChemBioChem
Volume 13, Issue 12, pages 1798–1804, August 13, 2012 DOI: 10.1002/cbic.201200187
Characterization of the Suillus grevillei Quinone Synthetase GreA Supports a Nonribosomal Code for Aromatic a-Keto Acids
Barbara Wackler 1, Dr. Gerald Lackner 1, Dr. Yit Heng Chooi 1, 2, Prof. Dr. Dirk Hoffmeister 1
1Friedrich-Schiller-Universitat, Department Pharmaceutical Biology at the Hans-Knoll-Institut, Beutenbergstrasse 11a, 07745 Jena (Germany)
2Current Address: University of California, Los Angeles, Department of Chemical and Biomolecular Engineering, Los Angeles, CA 90095 (USA)
... The DNA sequence of the combined insert sequences of these cosmids has been deposited
in GenBank (#JQ681152) and was submitted to FGENESH (Softberry, Mount Kisco, NY) and
to the BLAST server,29 to identify genes and exon/intron junctions. ...
The Plant Journal
Volume 72, Issue 1, pages 142–153, October 2012 DOI: 10.1111/j.1365-313X.2012.05072.x
The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements
Staton et al.,
1 Department of Genetics, University of Georgia, Athens, GA 30602, USA
2 Division of Biology, 426 Ackert Hall, Kansas State University, Manhattan, KS 66506, USA
... The bias in the EST matches to Gypsy elements, and the biased genomic abundance of these
sequences are shown in the tracks below the predicted genes. Gene predictions were made
using fgenesh (http://www.softberry.com) and maker (http://gmod.org/wiki/MAKER). ...
Chemistry & Biology
Volume 19, Issue 12, 21 December 2012, Pages 1611–1619 DOI: 10.1016/j.chembiol.2012.10.010
Terpendole E, a Kinesin Eg5 Inhibitor, Is a Key Biosynthetic Intermediate of Indole-Diterpenes in the Producing Fungus Chaunopycnis alba
Takayuki Motoyama1, Toshiaki Hayashi1, Hiroshi Hirota1, Masashi Ueki1, Hiroyuki Osada1
1 Chemical Biology Core Facility, Chemical Biology Department, RIKEN Advanced Science Institute, Wako-shi, Saitama 351-0198, Japan
... Nucleotide and amino acid sequence data were analyzed by DNASIS-Mac software (Hitachi
Software Engineering, Tokyo, Japan). Open reading frames were predicted by FGENESH and
FGENESH + software (Softberry, Mount Kiscko, NY). Construction of Recombinant Strains. ...
BMC Genomics
2012, 13:553 doi:10.1186/1471-2164-13-553
Sequencing of the core MHC region of black grouse (Tetrao tetrix) and comparative genomics of the galliform MHC
Biao Wang 1*, Robert Ekblom 2, Tanja M Strand 1,3, Silvia Portela-Bens 1 and Jacob Hoglund 1
1 Population Biology and Conservation Biology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18 D, Uppsala, SE-752 36, Sweden
2 Evolutionary Biology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18 D, Uppsala, SE-752 36, Sweden
... Identification of coding regions and putative exons was conducted by three different gene
prediction programs: Fgenesh ( http://www.softberry.com webcite), GeneMark.hmm (
http://exon.gatech.edu webcite) and Genscan ( http://genes.mit.edu/GENSCAN.html webcite) [ ...
PNAS
August 21, 2012 vol. 109 no. 34 13716-13721 DOI: 10.1073/pnas.1121096109
Rapid divergence and expansion of the X chromosome in papaya
Gschwend et al.,
aDepartment of Plant Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801;
bTexas AgriLife Research Center, Department of Plant Pathology and Microbiology, Texas A & M University, Weslaco, TX 78596;
... V. monoica Gene Prediction. Genes were predicted in the V. monoica BACs using Genscan
(http://genes.mit.edu/GENSCAN.html) and FGENESH (http://linux1.softberry.com/berry.phtml),
as well as homology to papaya-expressed sequence tags (ESTs) and gene models. ...
Theoretical and Applied Genetics
Volume 125, Issue 2 , pp 273-284 DOI: 10.1007/s00122-012-1832-8
Fine mapping of fw3.2 controlling fruit weight in tomato
Na Zhang, Marin Talbot Brewer, Esther van der Knaap
1. Department of Horticulture and Crop Science, The Ohio State University/OARDC, 217A Williams Hall, 1680 Madison Avenue, Wooster, OH, 44691, USA
2. Department of Plant Pathology, University of Georgia, Athens, GA, USA
... The sequence of the BAC C03Hba0051C24 encompassing fw3.2 was analyzed with the ab initio
gene prediction pro- grams FGENESH (http://www.softberry.com/berry.phtml) (Salamov and
Solovyev 2000) and is consistent with the recently released annotation of the tomato ...
BMC Genomics
2012, 13:444
http://www.biomedcentral.com/1471-2164/13/444 doi:10.1186/1471-2164-13-444
Comparative genomics of the white-rot fungi,
Phanerochaete carnosa and P. chrysosporium, to
elucidate the genetic basis of the distinct wood
types they colonize
Suzuki et al.,
1
Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
...Using the repeat-masked assembly, several gene prediction programs falling into three
general categories were used: 1) ab initio - FGENESH [52]; GeneMark [53], 2) homology-based - FGENESH+; Genewise [54] seeded by BLASTx alignments against GenBank’s database of non-redundant proteins (NR: [55]), and 3) EST-based - EST_map [56] seeded by EST contigs....
BMC Genomics
2012, 13:270
http://www.biomedcentral.com/1471-2164/13/270 doi:10.1186/1471-2164-13-270
The WRKY transcription factor family in Brachypodium distachyon
Tripathi et al.,
1
Department of Biology and Microbiology, South Dakota State University,
Brookings, SD 57007, USA
... Each potential gene was then manually curated using both FGENESH [38] and...
PLoS ONE
7(3): e32658. doi:10.1371/journal.pone.0032658
Membrane Topology and Predicted RNA-Binding Function of the ‘Early Responsive to Dehydration (ERD4)’ Plant Protein
Archana Rai, Penna Suprasanna, Stanislaus F. D'Souza, Vinay Kumar
Nuclear Agricultural & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
...Gene structure study was performed using popular gene finding pipeline (FGENESH at www.softberry.com)...
BMC Genomics
2012, 13:171 doi:10.1186/1471-2164-13-171
Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer
Hu et al.,
1 Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
2 Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
... Gene prediction, codon usage analysis & repetitive DNA identification. Gene prediction was
conducted using FGENESH [47], an ab initio gene predictor provided in the Softberry website.
A pre-trained Alternaria matrix was used to optimize predictions. ...
BMC Genomics
2012, 13:674 doi:10.1186/1471-2164-13-674
Design of a tobacco exon array with application to investigate the differential cadmium accumulation property in two tobacco varieties
Martin et al.,
1 Philip Morris International R&D, Philip Morris Products SA, Neuchatel 2000,
Switzerland
2 Institut fur Mathematik und Informatik, Greifswald D-17487, Germany
...FGENESH was trained for tobacco by SoftBerry Inc. and run as an ab initio gene finder with default parameters. Further
iterations of the tobacco genome assembly were also ...
The Plant Journal
Volume 72, Issue 2, pages 212–221, October 2012 DOI: 10.1111/j.1365-313X.2012.05059.x
Dynamic evolution of bz orthologous regions in the Andropogoneae and other grasses
Qinghua Wang 1, Hugo K. Dooner 1,2
1 Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
2 Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA
... The Fgenesh gene prediction program (http://www.softberry.com) was used to annotate
the non-orthologous genes in Coix and sorghum, and adjustment of exon/intron structures
was based on the sorghum and rice transcript annotation. ...
Plant Physiology
July 2012 vol. 159 no. 3 1086-1098 doi: http://dx.doi.org/10.1104/pp.112.197483
Altered Chloroplast Development and Delayed Fruit Ripening Caused by Mutations in a Zinc Metalloprotease at the lutescent2 Locus of Tomato
Barry et al.,
Department of Horticulture, Michigan State University, East Lansing, Michigan 48824 (C.S.B., Q.M.)
Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (G.M.A., R.P.M., J.J.G.)
...The prediction of genes within genomic DNA sequence was performed using the FGENESH hidden Markov model-based gene structure prediction program (http://linux1.softberry.com/berry.phtml). ...
Front Plant Sci.
2012; 3: 5. DOI: 10.3389/fpls.2012.00005
TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes
Leroy et al.,
1 UMR 1095, Genetics, Diversity and Ecophysiology of Cereals, Institut National de la Recherche Agronomique-Universite Blaise Pascal, Clermont-Ferrand, France
2 National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
For ab initio gene prediction, TriAnnot uses four programs: FGeneSH [17], GeneID (Guigo et al., 1992), GeneMarkHMM
BMC Plant Biology
2012, 12:20 doi:10.1186/1471-2229-12-20
Comparative transcriptome analysis of stylar canal cells identifies novel candidate genes implicated in the self-incompatibility response of Citrus clementina
Caruso et al.,
1 Dipartimento di Scienze delle Produzioni Agrarie e Alimentari, Universita degli Studi di Catania, Via Valdisavoia 5, 95123 Catania, Italy
2 Institut Valencia d'Investigacions Agraries - Centre de Genomica, Carretera Montcada de l'Horta-Naquera Km. 4,5, 46113 Montcada de l'Horta (Valencia), Spain
...ORF prediction was based on the genome browser data for each analyzed species as
well as Fgenesh analysis http://www.softberry.com...
PLoS ONE
7(2): e32010. doi:10.1371/journal.pone.0032010
A Highly Conserved, Small LTR Retrotransposon that Preferentially Targets Genes in Grass Genomes
Gao D, Chen J, Chen M, Meyers BC, Jackson S
Center for Applied Genetic Technologies and Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia, United States of America
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
...To predict the sequences in sorghum and maize, 20 kb of flanking sequence (10 kb on each side of the
transposon) were analyzed by the FGENESH (http://linux1.softberry.com) and the GeneMark.hmm ...
PLoS Pathog
8(9): e1002952. doi:10.1371/journal.ppat.1002952
Comparative Pathogenomics Reveals Horizontally Acquired Novel Virulence Genes in Fungi Infecting Cereal Hosts
Gardiner DM et al.,
Commonwealth Scientific and Industrial Research Organization (CSIRO) Plant Industry, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
...Protein coding genes were ab initio predicted in the F. pseudograminearum genome
using FGENESH [52] based on the F. graminearum gene models as part of the MolQuest2 package from Softberry, AUGUSTUS [53] and GeneMark-ES...
PLoS ONE
7(2): e31149. doi:10.1371/journal.pone.0031149
Genome-Wide Identification, Evolutionary Expansion, and Expression Profile of Homeodomain-Leucine Zipper Gene Family in Poplar (Populus trichocarpa)
Hu et al.,
CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and BioProcess Technology, Chinese Academy of Sciences, Qingdao, Shandong, People's Republic of China
... For the misannotated genes, manual reannotation was performed using online web server FGENESH (http://linux1.softberry.com/berry.phtml). ...
Theoretical and Applied Genetics
Volume 125, Issue 5 , pp 1047-1055 DOI 10.1007/s00122-012-1894-7
The isolation of Pi1, an allele at the Pik locus which confers broad spectrum resistance to rice blast
Lixia Hua et al.,
1. State Key Laboratory for Conservation and Utilization of Subtropic Agrobioresources, Laboratory of Plant Resistance and Genetics, College of Natural Resources and Environmental Sciences, South China Agricultural University, Guangzhou, 510642, China
2. National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
... The gene annotation tools RiceGAAS (http://ricegaas.dna.affrc. go.jp) and FGENESH
(http://www.softberry.com) were then used to identify Pi1 candidates within the 277-kb segment
of cv. Nipponbare defined by the closest flanking markers (CRG11-7 and K28). ...
Bioresource Technology
Volume 121, October 2012, Pages 404–410 http://dx.doi.org/10.1016/j.biortech.2012.07.027
Two neutral thermostable cellulases from Phialophora sp. G5 act synergistically in the hydrolysis of filter paper
Junqi Zhao et al.,
Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
... Transcription initiation sites and intron and exon information were predicted using the online
software FGENESH (http://linux1.softberry.com/berry.phtml). The presence of signal peptides
was predicted using SignalP 4.0 (http://www.cbs.dtu.dk/services/SignalP/). ...
Theoretical and Applied Genetics
Volume 125, Issue 4 , pp 773-779 DOI 10.1007/s00122-012-1870-2
Fine mapping and candidate gene analysis of the nuclear restorer gene Rfp for pol CMS in rapeseed (Brassica napus L.)
Zhi Liu et al.,
1. National Key Lab of Crop Genetic Improvement, National Center of Rapeseed Improvement (Wuhan Branch), Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China
... Candidate gene identification and sequence analysis The online system FGENESH
(http://www.softberry.com) was used to identify predicted ORFs in the delimited gene region. ... b
Candidate region of the Rfp locus and the predicted gene from http://www.softberry. com. ...
Plant Molecular Biology Reporter
Volume 30, Issue 4 , pp 1025-1031 DOI 10.1007/s11105-011-0408-0
Identification and Association Analysis of Castor Bean Orthologous Candidate Gene-Based Markers for High Oil Content in Jatropha curcas
Arti Sharma (1)
Rajinder Singh Chauhan (1)
1. Department of Biotechnology & Bioinformatics, Jaypee University of Information Technology, Waknaghat, P.O. Dumehar Bani, Kandaghat, Solan, 173 215, HP, India
... gene sequences from other plants (Arabidopsis, Brassica, Medicago, sunflower, soybean, and
cotton) were downloaded and annotated for open reading frames, including the 5? and 3?UTRs
using gene prediction algorithms of FGenesH (http://sun1.softberry.com/berry. ...
The Journal of Biological Chemistry
doi: 10.1074/jbc.M111.317982 January 6, 2012, 287, 1371-1380.
Biochemical Characterization of Indole Prenyltransferases
FILLING THE LAST GAP OF PRENYLATION POSITIONS BY A 5-DIMETHYLALLYLTRYPTOPHAN SYNTHASE FROM ASPERGILLUS CLAVATUS
Xia Yu ‡,1,
Yan Liu ‡§,2,
Xiulan Xie ¶,
Xiao-Dong Zheng § and
Shu-Ming Li ‡,3
From the ‡Institut fur Pharmazeutische Biologie und Biotechnologie, Philipps-Universitat Marburg, Deutschhausstrasse 17A, 35037 Marburg, Germany,
the §Department of Food Science and Nutrition, Zhejiang University, 310058 Hangzhou, Zhejiang, China, and
the ¶Fachbereich Chemie, Philipps-Universitat Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany
... gov). FGENESH from Softberry and the DNASIS software package (version 2.1, Hitachi
Software Engineering, San Bruno, CA) were used for exon prediction and sequence
analysis, respectively. Chemicals. Dimethylallyl diphosphate ...
Functional & Integrative Genomics
Volume 12, Issue 3 , pp 489-500 DOI
10.1007/s10142-012-0283-2
New cis-regulatory elements in the Rht-D1b locus region of wheat
Jialei Duan et al.,
1. College of Biology Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, 100094, Beijing, People’s Republic of China
... usda.gov/ITMI/Repeats/gene_annotation.pdf). Gene pre- dictions were accomplished
mainly by using the program FGENESH with the monocot (corn, rice, wheat, and
barley) training set (http://www.softberry.com). GENSCANW ...
Molecules and Cells
Volume 33, Issue 4 , pp 415-422 DOI
10.1007/s10059-012-0017-2
Ectopic expression of Capsicum-specific cell wall protein Capsicum annuum senescence-delaying 1 (CaSD1) delays senescence and induces trichome formation in Nicotiana benthamiana
Eunyoung Seo et al.,
2. Department of Plant Science, Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, Korea
1. Seeders Inc., Daejeon, 305-509, Korea
... an- nuum 'CM334' (Yoo et al., 2003). Both the gene-coding region and the 3?
untranslated region were predicted using the FGENESH program (http://linux1.
softberry.com/berry.phtml). Gene-specific primers were designed for ...
Mol Biol Evol
(2012) 29 (1): 91-100. doi: 10.1093/molbev/msr149
Ancestral Ca2+ Signaling Machinery in Early Animal and Fungal Evolution
Xinjiang Cai *,1 and
David E. Clapham * 2,3
1Molecular Pathogenesis Program, The Skirball Institute of Biomolecular Medicine, New York University Langone Medical Center
2Howard Hughes Medical Institute, Department of Cardiology, Children's Hospital Boston
3Department of Neurobiology, Harvard Medical School
... 2005) and FGENESH programs (http://www.softberry.com/berry.phtml?topic=index&group=
programs&subgroup=gfind) were used to predict the genes of interest by using identified
DNA segments and their neighboring regions of genomic sequences. ...
POJ
5(2):94-102 (2012)
Genome-wide analysis of cytosolic and chloroplastic isoforms of glutathione reductase in plant cells
Ahmad Tahmasebi 1, Farzaneh Aram 2, Mansour Ebrahimi 3, Manijeh Mohammadi-Dehcheshmeh 4,
Esmaeil Ebrahimie 1&5*
1Department of Crop Production & Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran
2Institute of Biotechnology, College of Agriculture, Shiraz University, Shiraz University, Shiraz, Iran
...Genomic sequences were also analyzed in the
FGENESH gene structure prediction program
(http://www.softberry.com) and GeneMark program
(http://opal.biology.gatech.edu/GeneMark)....
...Protein sorting and subcellular localization predictions were
performed according to ProtComp program Version 5
(http://www.softberry.com/)...
Phytopathology
May 2012, Volume 102, Number 5
Pages 506-518
http://dx.doi.org/10.1094/PHYTO-06-11-0180
Evidence for Morphological, Vegetative, Genetic, and Mating-Type Diversity in Sclerotinia homoeocarpa
Daniele Liberti, Jeffrey A. Rollins, and Philip F. Harmon
Department of Plant Pathology, 1453 Fifield Hall, University of Florida, Gainesville 32611.
... analysis. Protein prediction analysis was performed using ab initio gene prediction
software FGENESH (36) running on the Softberry web interface (http://
www.softberry.com) selecting S. sclerotiorum as the reference ge- nome. ...
Phytopathology
February 2012, Volume 102, Number 2
Pages 222-228
http://dx.doi.org/10.1094/PHYTO-03-11-0075
Identification and Fine-Mapping of Xa33, a Novel Gene for Resistance to Xanthomonas oryzae pv. oryzae
P. Natraj Kumar et al.,
Directorate of Rice Research, Rajendranagar, Hyderabad 500 030, India.
... Identification of putative candidate genes. The genomic se- quence between the flanking
SSR markers was downloaded from Japonica rice genome and analyzed using the online
software FGENESH (http://www.softberry.com). ... softberry.com). ...
Plant and Soil
July 2012, DOI
10.1007/s11104-012-1345-x
The genomic organization and transcriptional pattern of genes encoding nitrate transporters 1 (NRT1) in cucumber
M. Migocka,
A. Warzybok,
G. Klobus
1. Institute of Experimental Biology, Department of Plant Physiology, Wroclaw University, Kanonia 6/8, 50-328, Wroclaw, Poland
... AtNRT1 cDNAs were retrieved from the database and further analyzed using FGENESH and
FGENESH+ tools (Softberry, Inc., Mount Kisco, New York; www. ... The structure of each gene was
determined using FGENESH or FGENESH+ programs available on softberry.com ...
Molecular Genetics and Genomics
Volume 287, Issue 4 , pp 295-311 DOI
10.1007/s00438-012-0675-y
Genome-wide analysis of Aux/IAA gene family in Solanaceae species using tomato as a model
Jian Wu et al.,
1. Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, 310058, Hangzhou, People’s Republic of China
... After searching for IAA genes, bioinformatics tools, such as DNASTAR and FGENESH
(http://linux1.softberry.com/berry) were used to analyze and predict those unknown IAAs.
Isolation of the open reading frame (ORF) cDNA sequences ...
Gene
Volume 499, Issue 1, 10 May 2012, Pages 108–120
http://dx.doi.org/10.1016/j.gene.2012.01.048
Genome-wide analysis of the mitogen-activated protein kinase gene family in Solanum lycopersicum
Fuling Kong et al.,
Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou 310058, People's Republic of China
... After searching for MAPK gene family, DNASTAR and FGENESH (http://linux1.softberry.com/berry)
were used to analyze and predict those MAPK domains. ... Each predicted SlMAPK sequence was
confirmed by FGENESH (http://www.softberry.com/berry.phtml?topic=fgenesh). ...
Journal of Integrative Plant Biology
Volume 54, Issue 5, pages 321–329, May 2012 DOI: 10.1111/j.1744-7909.2012.01112.x
Identification and Fine Mapping of rhm1 Locus for Resistance to Southern Corn Leaf Blight in Maize
Yuanzeng Zhao et al.,
1
State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
2
Department of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
... region contains only one putative protein-coding gene using the FGENESH gene prediction
program (http://linux1.softberry.com/berry.phtml). This predicted gene was a homologue of ... monocot
training set (http://linux1.softberry.com/berry.phtml). The predicted genes were ...
Theoretical and Applied Genetics
September 2012 DOI
10.1007/s00122-012-1975-7
Fine mapping and characterization of BPH27, a brown planthopper resistance gene from wild rice (Oryza rufipogon Griff.)
D. Huang et al.,
1. State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Agricultural College, Guangxi University, Nanning, 530005, China
2. Rice Research Institute, Plant Protection Institute and Guangxi Rice Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
... The putative open reading frame (ORF) in the target region was predicted by the online
software GENESCAN and FGENESH of Softberry (www.softberry.com/berry.phtml) with
monocot plants as the model organism. Host selection behavior ...
Gene
Volume 507, Issue 1, 1 October 2012, Pages 54–60 http://dx.doi.org/10.1016/j.gene.2012.07.004,
Characterization of Aquilegia Polycomb Repressive Complex 2 homologs reveals absence of imprinting
Emily J. Gleason a, b,
Elena M. Kramer a,
a Dept. of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave. Cambridge, MA, 02138, USA
b Dept. of Molecular and Cellular Biology, Harvard University, 16 Divinity Ave. Cambridge, MA, 02138, USA
... the query sequence. We then used the SoftBerry FGENESH program (http://linux1.
softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind) to predict
open reading frames for the loci. cDNA sequences were ...
African Journal of Biotechnology
Vol. 11(40), pp. 9534-9542, 17 May, 2012 DOI: 10.5897/AJB12.040
Isolation and characterization of a candidate gene for
resistance to cereal cyst nematode from Aegilops
variabilis in China
D. L. Xu et al.,
1
Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China.
2
Graduate University of the Chinese Academy of Sciences, Beijing, China.
... The ORFs of the sequences were identified by FGENESH (http://linux1.softberry.com/) and the
amino acid sequence was obtained at the same time. ... The resulting sequences were analyzed
using NSITE-PL to identify regulatory motifs (http://linux1.softberry.com/). RESULTS ...
Theoretical and Applied Genetics
Volume 125, Issue 6 , pp 1125-1135 DOI
10.1007/s00122-012-1899-2
Characterization, fine mapping and expression profiling of Ragged leaves1 in maize
Haiying Guan et al.,
1. Department of Plant Genetics and Breeding, State Key Laboratory of Agrobiotechnology and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
2. Department of Life Science and Technology, Henan Institute of Science and Technology, XinXiang, 453003, China
... 2004). The gene prediction was conducted by Softberry (http://linux1.softberry.com/berry.
phtml?topic=fgenesh&group=programs&subgroup=gfind). Transcriptome sequencing and gene
annotation The BC3 segregating population was grown in a green- house. ...
Molecular Genetics and Genomics
Volume 287, Issue 3 , pp 247-259 DOI
10.1007/s00438-012-0674-z
Candidate genes within a 143 kb region of the flower sex locus in Vitis
Iris Fechter et al.,
1. Julius Kuhn-Institut, Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, 76833, Siebeldingen, Germany
2. Center for Biotechnology, Bielefeld University, 33594, Bielefeld, Germany
... PCR amplifications were per- formed to ensure order of contigs in cases of
uncertainties. Gene prediction The sequences were annotated from the scaffolds
using the software FGENESH (http://linux1.softberry.com/berry. phtml). ...
Braz. J. Plant Physiol.,
24(1): 69-73, 2012
Isolation and in silico characterization of cDNA encoding
cyclophilin from etiolated Vigna mungo seedlings
Kalika Kuhar
1
, Varun Kumar Gupta
1
, Rekha Kansal
2
, Vijay Kumar Gupta
1
*
1
Department of Biochemistry, Kurukshetra University, Kurukshetra, Haryana, India.
2
National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (PUSA), New Delhi, India.
... The nucleotide sequence was analyzed in silico using VecScreen program of National
Center for Biotechnology Information (NCBI), Basic Local Alignment Search Tool (BLAST),
FGENESH program of Softberry web server and BioEdit. ...
Mol Biol Evol
2012, 29 (2): 631-645.
doi: 10.1093/molbev/msr208
Zisupton—A Novel Superfamily of DNA Transposable Elements Recently Active in Fish
Astrid Bohne et al.,
1Institut de Genomique Fonctionnelle de Lyon, Universite de Lyon, Universite Lyon 1, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Ecole Normale Superieure de Lyon, Lyon, France
2Department of Physiological Chemistry I, Biocenter, University of Wurzburg, Wurzburg, Germany
... 10 ?05 . Automatic sequence annotation was refined manually using expressed
sequence tag data and related protein sequences with the help of FGENESH on
the softberry web server (http://linux1.softberry.com). Nucleotide ...
3 Biotech.
2012 September; 2(3): 199–209. Published online 2012 March 24. doi: 10.1007/s13205-012-0047-7
Cloning, characterization and expression analysis of a novel gene encoding Kunitz-type protease inhibitor from Dolichos biflorus
Kalika Kuhar,1 Rekha Kansal,2 Amit Mishra,2 Kirpa Ram Koundal,2 and Vijay Kumar Gupta 1
1Department of Biochemistry, Kurukshetra University, Kurukshetra, Haryana India
2National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (PUSA), New Delhi, India
... The primers were designed from the coding region of the genes determined through Softberry
software following the standard rules and analyzed using Fast PCR software for self-dimers,
melting temperature ... 2) as predicted by FGENESH program of Softberry web server. ...
Immunogenetics
2011 Nov;63(11):753-71. doi: 10.1007/s00251-011-0549-1. Epub 2011 Jun 28.
Defining the turkey MHC: identification of expressed class I- and class IIB-like genes independent of the MHC-B
Reed et al.,
Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108, USA
... Final assembly of repeated contigs was confirmed by PCR and resequencing. Gene identification
and annotation Sequences were analyzed with Softberry FGENESH and BLAST
(http://linux1.softberry.com/all.htm) to identify putative transcripts and homologies to known genes. ...
Journal of Insect Physiology
Volume 58, Issue 4, April 2012, Pages 570–579 DOI: 10.1016/j.jinsphys.2011.12.009
Localization of two Na+- or K+-H+ antiporters, AgNHA1 and AgNHA2, in Anopheles gambiae larval Malpighian tubules and the functional expression of AgNHA2 in yeast
Minghui A. Xiang a, c, Paul J. Linser b, David A. Price b, William R. Harvey b, c, d, e
a Division of Nephrology and Hypertension, Department of Medicine, University of Florida-Jacksonville, Jacksonville, FL 32206, USA
b Whitney Mosquito Biology Group, University of Florida, 9505 Ocean Shore Boulevard, St. Augustine, FL 32080, USA
... gambiae that were applied to FGENESH at the Softberry site (http://www.softberry.com/berry.phtml)
identified a cDNA from a genomic region of 30 kb; it included the originally predicted cDNA
exons and predicted two more exons at the 5? end although it had the same 3 ...
BMC Proceedings
2011, 5(Suppl 7):P65 doi:10.1186/1753-6561-5-S7-P65
Genome characterization of a Eucalyptus natural mutant
Fuchs et al.,
1 Departamento de Genetica, Instituto de Biociencias, Universidade Estadual Paulista (UNESP), Distrito de Rubiao Jr s/n CEP 18618-000, Botucatu (SP), Brazil
2 Departamento de Genetica, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), Universidade de Sao Paulo (USP), Avenida Padua Dias, 11 CEP 13418-900, Piracicaba (SP), Brazil
... phytozome.net/ webcite) using BLAST. The genomic region identified was analyzed
by FGENESH tool (Softberry, Inc. – http://www.softberry.com webcite) to find predicted
genes in the region. Predicted genes were translated ...
Journal of Insect Physiology
Volume 57, Issue 9, September 2011, Pages 1190–1197 DOI: 10.1016/j.jinsphys.2011.05.011
Functions of duplicated genes encoding CCAP receptors in the red flour beetle, Tribolium castaneum
Bin Li a, 1, Richard W. Beeman b, Yoonseong Park a
a Department of Entomology, Waters Hall, Kansas State University, Manhattan, KS 66506, USA
b USDA-ARS Center for Grain and Animal Health Research, 1515 College Avenue, Manhattan, KS 66502, USA
... Initial search results were further analyzed using the gene prediction software FGENESH
(http://linux1.softberry.com/berry.phtml). Similar methods were used to mine candidate CCAP
receptors from other insect genomes for comparisons of gene structures and sequences. ...
Funct Integr Genomics.
2011 Dec;11(4):599-609. doi: 10.1007/s10142-011-0237-0. Epub 2011 Jul 16.
Recent insertion of a 52-kb mitochondrial DNA segment in the wheat lineage
Zhang J, Jia J, Breen J, Kong X.
Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Science, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, People's Republic of China
... plot analysis (Krumsiek et al. 2007). Gene prediction and function assignment Gene
prediction was performed using FGENESH at softberry web site (http://www.softberry.
com) and GENES- CAN. Then, BLASTP against the non ...
Fungal Biology
Volume 116, Issue 2, February 2012, Pages 225–233 DOI: 10.1016/j.funbio.2011.11.005
mrflbA, encoding a putative FlbA, is involved in aerial hyphal development and secondary metabolite production in Monascus ruber M-7
Yishan Yang c, Li Li c, Xin Li c, Yanchun Shao a, c, Fusheng Chen a, b, c,
a State Key Laboratory of Agricultural Microbiology, Wuhan 430070, Hubei Province, PR China
b Key Laboratory of Food Safety Evaluation of the Ministry of Agriculture, Wuhan 430070, Hubei Province, PR China
... Specific primers for 3'RACE were designed according to the predicted cDNA sequence of the
mrflbA or mga1 gene using SoftBerry's FGENESH program (http://linuxl.softberry.com/ berry.phtml),
while primers for 5'RACE were designed according to the sequences obtained by 3 ...
Breast Cancer Research and Treatment
Volume 130, Issue 3 , pp 1003-1010 DOI: 10.1007/s10549-011-1677-x
Further evidence for the contribution of the RAD51C gene in hereditary breast and ovarian cancer susceptibility
Vuorela et al.,
1. Laboratory of Cancer Genetics, Department of Clinical Genetics and Biocenter Oulu, University of Oulu, Oulu University Hospital, P.O. Box 5000, 90014, Oulu, Finland
2. Department of Pathology and Forensic Medicine, School of Medicine, Institute of Clinical Medicine, University of Eastern Finland, 70211, Kuopio, Finland
... 2). According to FPROM human promoter prediction software (Softberry, Inc., Mt. ... FGENESH
(Softberry, Inc., Mt. Kisco, NY), are abolished. Based on bioinformatics, the observed
27 bp deletion thus produces a null allele, and is pathogenic. ...
Biologia Plantarum
Volume 55, Issue 4 , pp 614-624 DOI: 10.1007/s10535-011-0159-7
Molecular cloning and phylogenetic analysis of cereal type II metacaspase cDNA from wheat
E. Piszczek, M. Dudkiewicz, M. Sobczak
1. Department of Biochemistry, Warsaw University of Life Sciences, 159 Nowoursynowska, PL-02776, Warsaw, Poland
2. Department of Experimental Design and Bioinformatics, Warsaw University of Life Sciences, 159 Nowoursynowska, PL-02776, Warsaw, Poland
... The identification of the coding region, open reading frame and the translation of TaeMCAII
nucleotide sequence were made based on the FGENESH gene structure prediction using an
HMM model constructed for monocot plants (SoftBerry software http://linux1.softberry.com ...
Plant Cell Reports
Volume 30, Issue 11 , pp 2059-2073 DOI: 10.1007/s00299-011-1113-z
Identification, isolation and expression analysis of auxin response factor (ARF) genes in Solanum lycopersicum
J. Wu et al.,
1. Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Hangzhou, 310058, People’s Republic of China
2. Department of Horticulture, Zhejiang University, Hangzhou, 310058, People’s Republic of China
... databases. After searching for ARF genes, bioinformatics tools, such as DNASTAR and
FGENESH (http://linux1.softberry.com/berry) were used to analyze and predict those
unknown SlARFs. ... www. softberry.com/berry.phtml?topic=fgenesh). ...
Sains Malaysiana
40 (4). pp. 331-337. ISSN 0126-6039
Cloning and analysis of pyrG gene encoding orotidine 5-Monophosphate decarboxylase of aspergillus oryzaeStrain S1
Selina Oh Siew Ling, and Leong , Jiun Min and Abdul Munir Abdul Murad, and Nor Muhammad Mahadi , and Farah Diba Abu Bakar
BGI
... 475 bp). The pyrG contained one intron at position 623-687 bp based on the
AUGUSTUS and FGENESH (SoftBerry) analysis corresponding to the intron present
in the pyrG of A. oryzae (Accession Number: Y13811). In silico ...
Nucl. Acids Res.
(2011) 39 (suppl 1): D637-D639.
doi: 10.1093/nar/gkq1016
FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum
Wong et al.,
1Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology, Ingolstadter Landstrasse 1, D-85764 Neuherberg, 2Max-Planck-Institute for Terrestrial Microbiology, Department of Organismic Interactions, D-35043 Marburg
... Based on this set, all gene loci in FGDB v3.1 were re-annotated using a pipeline including (i)
Fgenesh with different matrices (www.softberry.com); (ii) GeneMark-ES (8); (iii) Augustus with
ESTs, precedingly annotated Fusarium models and/or Neurospora crassa protein ...
Theoretical and Applied Genetics
Volume 123, Issue 4 , pp 625-633 DOI: 10.1007/s00122-011-1612-x
Fine-mapping of the woolly gene controlling multicellular trichome formation and embryonic development in tomato
Changxian Yang, Hanxia Li, Junhong Zhang, Taotao Wang, Zhibiao Ye
1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
2. Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
... Protein coding genes were predicted from the resul- tant contig using the FGENESH program
(http://linux1.soft- berry.com/berry.phtml). ... Analysis of the »200 kb sequence revealed that this
fragment contains 19 ORFs as automatically predicted by FGENESH (http://softberry. ...
POJ
4(5):239-249(2011)
Comparative analysis of the genomic regions flanking Xa21 locus in indica and japonica ssp.
of rice (Oryza sativa L.)
Kumar et al.,
1Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli Prof. C.R. Rao
Road , Hyderabad 500046, India
2Department of Plant Pathology, Directorate of Rice Research, Rajendranagar, Hyderabad 500030, India
... Protcomp V 8.0 (http://linux1.softberry.com/ berry.phtml) analysis for the sub cellular location of
proteins showed that 80% of the predicted TEs were nuclear in localization while the remaining
were cytoplasmic or mitochondrial in both the rice lines (Table 9). GC Content in the ...
...Gene prediction from the 100 kb region flanking to Xa21
locus of chromosome 11 in japonica and indica rice was
carried out using HMM based gene structure prediction
software FGENESH tool (www.softberry.com) trained for
monocot plant species (Salamov and Solovyer, 2000) ...
Eukaryotic Cell
doi: 10.1128/EC.05255-11 December 2011 vol. 10 no. 12 1740-1741
Draft Genome Sequence of Penicillium marneffei Strain PM1
Woo et al.,
1Department of Microbiology
2State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong
... genome, were sequenced. The Phred/Phrap/Consed software package was used
for base calling and sequence assembly (1,–,5). Protein-coding genes and introns
were predicted using FGENESH (Softberry). The draft genome ...
Theoretical and Applied Genetics
Volume 122, Issue 5 , pp 1017-1028 DOI: 10.1007/s00122-010-1506-3
The Pik-p resistance to Magnaporthe oryzae in rice is mediated by a pair of closely linked CC-NBS-LRR genes
Yuan et al.,
1. Laboratory of Plant Resistance and Genetics, College of Resources and Environmental Sciences, South China Agricultural University, Guangzhou, 510642, China
2. Hubei Academy of Agricultural Science, Wuhan, 430064, China
... Wang et al. 2009). The gene content in the equivalent interval of cv. Nipponbare
was predicted using GENESCAN (http://genes.mit.edu/ GENSCAN.html) and
FGENESH (http://www.softberry. com). DNA sequence comparisons ...
BMC Proceedings
2011, 5(Suppl 7):O17 doi:10.1186/1753-6561-5-S7-O17
High-throughput targeted SNP discovery using Next Generation Sequencing (NGS) in few selected candidate genes in Eucalyptus camaldulensis
Prasad S Hendre *, Rathinam Kamalakannan, Rathinavelu Rajkumar and Mohan Varghese
ITC R&D Centre, Peenya Insdustrial Area, No.3, 1st Main, 1st Phase, Bangalore- 560 058, Karnataka, India
... block. Web-based gene prediction tool FGENESH (http://linux1.softberry.com webcite)
was used for identifying genic regions such as UTRs, exons and introns with
Arabidopsis thaliana gene model. Results and discussion. Forty ...
Fungal Biology
Volume 115, Issue 8, August 2011, Pages 775–781 DOI: 10.1016/j.funbio.2011.06.002,
Characterisation of the ArmA adenylation domain implies a more diverse secondary metabolism in the genus Armillaria
Mathias Misiek, Jana Braesel, Dirk Hoffmeister
Friedrich-Schiller-Universitat Jena, Department Pharmaceutical Biology at the Hans-Knoll-Institute, Beutenbergstrasse 11a, 07745 Jena, Germany
... The Aspergillus, Laccaria, or Phanerochaete search algorithms of FGENESH (Softberry, Mount
Kisco, NY) were used to predict gene structures and exon/intron junctions in the insert sequences
of three previously identified Armillaria cosmids 108, 138, and 152 (Misiek & ...
Mol Biol Evol
(2011) 28 (6): 1913-1926. doi: 10.1093/molbev/msr012
Molecular Evolution of the Metazoan PHD–HIF Oxygen-Sensing System
Kalle T. Rytkonen *,1, Tom A. Williams 2, Gillian M. Renshaw 3, Craig R. Primmer 1 and Mikko Nikinmaa 1
1Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
2Department of Genetics, University of Dublin, Trinity College, Dublin, Ireland
... surrounding the primary BlastP hits in the genome contigs and repredicted the gene structure
using three independent pieces of software: GENESCAN (http://genes.mit.edu/GENSCAN.html),
Augustus (http://augustus.gobics.de/), and FGENESH (http://linux1.softberry.com). ...
Theoretical and Applied Genetics
Volume 123, Issue 4 , pp 585-601 DOI: 10.1007/s00122-011-1609-5
Towards an understanding of the nature of resistance to Phytophthora root rot in red raspberry
Graham et al.,
1. Genetics Department, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
2. Biomathematics and Statistics Scotland, Invergowrie, Dundee, DD2 5DA, Scotland, UK
... Gene prediction Open reading frames from both BAC sequences were identified
using the Softberry gene structure prediction program FGENESH (http://linux1.
softberry.com/berry. phtml) using Vitis vinifera as the reference. ...
Applied Microbiology and Biotechnology
Volume 89, Issue 6 , pp 1851-1858 DOI: 10.1007/s00253-010-3016-2
An acid and highly thermostable xylanase from Phialophora sp. G5
Zhang et al.,
1. Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, China
2. School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
... ncbi.him.nih.gov/gorf/gorf/gorf.html). Genes, introns, exons and transcription initiation sites were
predicted using the online software FGENESH (http://linux1.softberry.com/ berry.phtml). The signal
peptide was predicted using SignalP (http://www.cbs.dtu.dk/services/SignalP/). ...
Experimental Parasitology
Volume 127, Issue 1, January 2011, Pages 184–194 DOI: 10.1016/j.exppara.2010.07.012
Identification of papain-like cysteine proteases from the bovine piroplasm Babesia bigemina and evolutionary relationship of piroplasms C1 family of cysteine proteases
Tiago M. Martins a, b, , , Virgilio E. do Rosario b, Ana Domingos a, b
a Unidade de Tecnologias de Proteinas e Anticorpos Monoclonais, Instituto de Higiene e Medicina Tropical, Estrada do Paco do Lumiar 22, 1649-038 Lisboa, Portugal
b Centro de Malaria e Doencas Tropicais, Instituto de Higiene e Medicina Tropical, Rua da Junqueira 96, 1349-008 Lisboa, Portugal
... A threshold of E ? 1e-04 was adopted for the tblastn search (Wu et al., 2003). The gene
structure of the identified CP genes with multiple exons was predicted using the
FGENESH and FGENESH+ software (http://www.softberry.com). ...
Advanced Studies in Biology
Vol. 3, 2011, no. 4, 169 – 180
Genetic Disease Resistance and Conservation of a
Plant Gene that Encodes a Mitogen-Activated Protein
Kinase Kinase Kinase
L. David Kuykendall, Jonathan Y. Shao, Rachel P. Naegele and J. Mitchell McGrath
Molecular Plant Pathology Laboratory, Plant Sciences Institute Beltsville
Agricultural Research Center, Beltsville MD 20705, USA
Department of Crop and Soil Sciences and USDA-ARS
Sugar Beet and Bean Research, Michigan State University
East Lansing, MI 48824-1325,USA
...The sequence contig was screened for coding sequence using a
combination of the following programs:
GeneMark [21] for eukaryotes:(http://exon.gatech.edu/GeneMark/eukhmm.cgi),
GenScan [22] (http://genes.mit.edu/GENSCAN.html)
FGENESH (http://linux1.softberry.com/berry.phtml...
Comparative and Functional Genomics
Volume 2011 (2011), Article ID 286089, 9 pages
doi:10.1155/2011/286089
Repertoire of SSRs in the Castor Bean Genome and Their Utilization in Genetic Diversity Analysis in Jatropha curcas
Arti Sharma and Rajinder Singh Chauhan
Department of Biotechnology & Bioinformatics, Jaypee University of Information Technology, Waknaghat, P.O. Dumehar Bani, Kandaghat, Solan 173 215, India
... Castor bean genome sequence contigs harboring SSRs were annotated for putative open reading
frames, including 5?UTRs and 3?UTRs, using gene prediction algorithms of FGenesH
(http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind ...
Advanced Science Letters
Volume 4, Numbers 11-12, November 2011 , pp. 3653-3657(5) DOI: http://dx.doi.org/10.1166/asl.2011.2027
Cloning and Sequence Analysis of Candidate Disease Resistance Genes from Dongxiang Common Wild Rice (O. rufipogon Griff.)
Han, Xiaoxia et al.,
BGI
... The Genomic DNA Sequence Analysis DNA sequence location and similarity analysis was
performed by BLAST program (http://www.ncbi.nlm.nih.gov/).13 Gene pre- diction was performed
by FGENESH (Solovyev and Salamov 1999; http://www.softberry.com/berry.phtml) and ...
New Phytologist
2011, 192: 164–178. doi: 10.1111/j.1469-8137.2011.03800.x
Comparative analysis of peanut NBS-LRR gene clusters suggests evolutionary innovation among duplicated domains and erosion of gene microsynteny.
Ratnaparkhe et al.,
1 Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
2 Center for Genomics and Computational Biology, School of Life Sciences, School of Sciences, Hebei United University, Tangshan, Hebei 063000, China
... sequenced. Assembled sequences were visualized and manually edited using
Consed (Gordon et al., 1998). Peanut BAC sequences were annotated using gene
prediction programs FGENESH (http://www.softberry.com). The ...
Plant Molecular Biology Reporter
Volume 29, Issue 4 , pp 769-783 DOI: 10.1007/s11105-010-0284-z
Genome-Wide Analysis of Fatty Acid Desaturases in Soybean (Glycine max)
Xiaoyuan Chi et al.,
1. Shandong Peanut Research Institute, Qingdao, 266100, People’s Republic of China
2. Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, People’s Republic of China
... The searches were iterated until convergence. As for the incorrectly predicted genes,
manual reannotation was performed using online web server FGENESH
(http://linux1.softberry.com/berry.phtml; Salamov and Solovyev 2000). ...
Molecular Genetics and Genomics
Volume 285, Issue 1 , pp 79-90 DOI: 10.1007/s00438-010-0587-7
Relative evolutionary rates of NBS-encoding genes revealed by soybean segmental duplication
Xiaohui Zhang et al.,
1. State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
2. National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
... All new BLAST hits in the genomes, together with flanking regions of 5,000–10,000 bp at both
sides, were annotated using the gene-finding programs FGENESH with the legume plant training
set (http://www.softberry.com/) and GENSCAN with the Arabidopsis training set (http ...
Metabolic Engineering
Volume 13, Issue 6, November 2011, Pages 723–732 DOI: 10.1016/j.ymben.2011.09.008
Identification and engineering of the cytochalasin gene cluster from Aspergillus clavatus NRRL 1
Kangjian Qiao a, Yit-Heng Chooi a, Yi Tang a, b,
a Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, United States
b Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States
... Gene predictions were performed via FGENESH program (www.softberry.com) and manually
checked based on homologous gene/protein sequences in the GenBank database. Protein
domain functions were deduced using Conserved Domain Search (NCBI). 2.3. ...
International Journal of Plant Genomics
Volume 2011 (2011), Article ID 370548, 8 pages
doi:10.1155/2011/370548
Genes Encoding Callose Synthase and Phytochrome A Are Adjacent to a MAP3K?-Like Gene in Beta vulgaris US H20
L. David Kuykendall and Jonathan Y. Shao
Molecular Plant Pathology Laboratory, Agricultural Research Service, US Department of Agriculture, Plant Sciences Institute, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Building 004, Room 120, BARC-West, Beltsville, MD 20705, USA
... NCBI BLAST [8]. The 125 Kb sequence was screened for coding sequence using a combination
of the following programs: GeneMark [9, 10] for eukaryotes (http://exon.gatech.edu/GeneMark/
eukhmm.cgi), Augustus (http://augustus.gobics.de/), and FgenesH (http://softberry.com ...
BMC Plant Biology
2011, 11:44 doi:10.1186/1471-2229-11-44
Characterisation of the legume SERK-NIK gene superfamily including splice variants: Implications for development and defence
Kim E Nolan, Sergey Kurdyukov and Ray J Rose
Australian Research Council Centre of Excellence for Integrative Legume Research, School of Environmental and Life Sciences. The University of Newcastle. University Dr. Callaghan, NSW, 2308, Australia
... potential coding regions from the individual genomic sequences were predicted
using FGENESH software (Softberry; http://linux1.softberry.com webcite) ...
Journal of Bioscience and Bioengineering
Volume 112, Issue 6, December 2011, Pages 551–557 DOI: 10.1016/j.jbiosc.2011.08.018,
Acidic b-mannanase from Penicillium pinophilum C1: Cloning, characterization and assessment of its potential for animal feed application
Hongying Cai et al.,
Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
2 Department of Microbial Engineering, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
... Introns, exons and transcription initiation sites were predicted using the online software
FGENESH (http://linux1.softberry.com/berry.phtml). The signal peptide was predicted
using SignalP (http://www.cbs.dtu.dk/services/SignalP/). ...
Journal of Molecular Evolution
Volume 72, Issue 5-6 , pp 498-509 DOI: 10.1007/s00239-011-9448-1
Co-Variation Among Major Classes of LRR-Encoding Genes in Two Pairs of Plant Species
Jiao Wang, Shengjun Tan, Li Zhang, Ping Li, Dacheng Tian
1. State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
2. Rice Research Institute, Sichuan Agricultural University, Wenjiang, 611130, China
.. Their sequences and corresponding annotations were downloaded from the online databases
(Table S1). The annotation methods and quality could affect the gene identification. To estimate
the bias, we used the ab initio gene finder FGENESH (http://linux1.softberry. ...
New Phytologist
189: 321–334. doi: 10.1111/j.1469-8137.2010.03462.x
The isolation and characterization of Pik, a rice blast resistance gene which emerged after rice domestication.
Zhai et al.,
1 Laboratory of Plant Resistance and Genetics, College of Resources and Environmental Sciences, South China Agricultural University, Guangzhou, 510642, China
2 Rice Research Institute, Guangdong Provincial Academy of Agricultural Sciences, Guangzhou, 510640, China
... Candidate gene identification. The gene annotation tools RiceGAAS (http://ricegaas.dna.affrc.
go.jp) and FGENSH (http://www.softberry.com) were used to identify Pik candidates within the
166-kb segment of cv Nipponbare defined by the flanking markers K34 and K28 (Fig. 1a). ...
Process Biochemistry
Volume 46, Issue 12, December 2011, Pages 2341–2346 DOI: 10.1016/j.procbio.2011.09.018,
A novel thermoacidophilic family 10 xylanase from Penicillium pinophilum C1
Cai et al.,
Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
... The signal peptide was predicted using SignalP (http://www.cbs.dtu.dk/services/SignalP/). The
exon–intron structure and transcription initiation sites of the full-length gene were predicted using
the online software FGENESH (http://linux1.softberry.com/berry.phtml). ...
International Journal of Plant Genomics
Volume 2011 (2011), Article ID 291563, 12 pages
doi:10.1155/2011/291563
Comparative Genomics in Perennial Ryegrass (Lolium perenne L.): Identification and Characterisation of an Orthologue for the Rice Plant Architecture-Controlling Gene OsABCG5
Hiroshi Shinozuka, 1,2,3 Noel O. I. Cogan, 1,2,3 German C. Spangenberg, 1,2,3,4 and John W. Forster 1,2,3,4
1Biosciences Research Division, Department of Primary Industries, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, 1 Park Drive, Bundoora, VIC 3083, Australia
2Molecular Plant Breeding Cooperative Research Centre, Bundoora, VIC 3083, Australia
... Gene structure prediction was performed using the FGENESH program with the parameter setting
for monocot plants (http://linux1.softberry.com/berry.phtml). Phylogenetic analysis was performed
using the CLUSTALW program (http://www.genome.jp/tools/clustalw/). ...
Advanced Studies in Biology
Vol. 3, 2011, no. 1, 13 - 24
A Plant Gene Encodes a ‘HSFA9-like’ Heat Shock
Factor and is Part of a Cluster of Orthologous Genes
Including NPR1, CaMP and CK1 in Beta vulgaris,
Populus trichocarpa, Solanum lycopersicum
and Vitis vinifera
David Kuykendall, Jonathan Shao, Kate Burdekin and Lauren Conway
Molecular Plant Pathology Laboratory, PSI, BARC
10300 Baltimore Avenue, Beltsville, MD 20705 USA
...Putative genes in these genomic regions were annotated using FGenesH
program (Gene finding in Eukaryota, http://linux1.softberry.com/). ...
The Journal of Microbiology
Volume 49, Issue 3 , pp 473-480 DOI: 10.1007/s12275-011-0362-4
Isolation and characterization of a reducing polyketide synthase gene from the lichen-forming fungus Usnea longissima
Wang et al.,
1. Korean Lichen Research Institute, Sunchon National University, Sunchon, 540-742, Republic of Korea
... The potential open reading frame (ORF) of FoNRks2662 was scanned with FGENESH (Berg
et al., 2008) using Aspergillus as the matrix (http://linux1. softberry.com). The putative function
of these ORFs was determined using a basic local alignment search tool (BLAST). ...
Genome
2011, 54(12): 1041-1044, DOI: 10.1139/g11-068
Isolation of a strawberry gene fragment encoding an actin depolymerizing factor-like protein from genotypes resistant to Colletotrichum acutatum
Marta Ontivero, a Gustavo Martinez Zamor a,b Sergio Salazar, c Juan Carlos Diaz Ricci, b Atilio Pedro Castagnaro a
Seccion Biotecnologia, Estacion Experimental Agroindustrial Obispo Colombres-Unidad Asociada al INSIBIO, Av. William Cross 3150, 4101 Las Talitas, Tucuman, Argentina.
bInstituto Superior de Investigaciones Biologicas (INSIBIO; CONICET- UNT) and Instituto de Quimica Biologica “Dr. Bernabe Bloj”, Universidad Nacional de Tucuman. Chacabuco 461, 4000 Tucuman. Argentina.
... The deduced amino acid sequence showed identity scores ranging between 93% and 60%,
with E values comprised between 1 ? 10 –37 and 6 ? 10 –44 . The gene prediction programs
SPL and FGENESH 2.6 (www.softberry.com) (Solovyev et al. ...
Plant Molecular Biology
Volume 77, Issue 1-2 , pp 59-75 DOI: 10.1007/s11103-011-9794-9
BraSto, a Stowaway MITE from Brassica: recently active copies preferentially accumulate in the gene space
Veronique Sarilar, Anne Marmagne, Philippe Brabant, Johann Joets, Karine Alix
1. AgroParisTech/CNRS, UMR 0320/UMR 8120 Genetique Vegetale INRA/Univ. Paris-Sud/CNRS/AgroParisTech, Ferme du Moulon, 91190, Gif-sur-Yvette, France
2. CNRS, UMR 0320/UMR 8120 Genetique Vegetale INRA/Univ. Paris-Sud/CNRS/AgroParisTech, Ferme du Moulon, 91190, Gif-sur-Yvette, France
... We used a combination of FGENESH v.2.6 (http://linux1.softberry.com/berry.phtml?topic=
fgenesh&group=programs&subgroup=gfind, Salamov and Solovyev 2000), with arabidopsis
thaliana (arabidopsis) as the reference model, and BLASTP to characterize the genomic ...
Front Plant Sci.
2011; 2: 35. DOI: 10.3389/fpls.2011.00035
Mining Disease-Resistance Genes in Roses: Functional and Molecular Characterization of the Rdr1 Locus
Terefe-Ayana et al.,
1Institute for Plant Genetics, Leibniz University Hannover, Hannover, Germany
... Gene prediction and annotation. Bioedit (Hall, 1999) was used for viewing and editing of
sequences. Gene prediction and annotation was done using the gene prediction programs
FGENESH and GENSCAN (http://www.softberry.com; http://genes.mit.edu/GENSCAN.html). ...
Journal of Plant Genetics and Transgenics
Vol 2, No 1 (2011) Chandel
In Silico Expression Analysis of QTL Specific Candidate Genes for Grain Micronutrient (Fe/Zn) Content Using ESTs and MPSS Signature Analysis in Rice (Oryza sativa L.)
Girish Chandel, P. Samuel, M. Dubey, R. Meena
BGI
... The nucleotide sequences were downloaded and analyzed for open reading frames (ORFs)
and the CDS (Coding DNA sequence) using gene prediction algorithms of FGenesH
(http://sun1.softberry.com/berry.phtml?topic=fgenesh&group =programs&subgroup=gfin). ...
Plant Physiology
March 2011 vol. 155 no. 3 1301-1311 DOI: 10.1104/pp.110.168500
Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domesticationome
Zhu et al.,
National Center for Gene Research and Institute of Plant Physiology and Ecology (B.-F.Z., L.S., Y.Z., J.Z., Y.S., D.L., D.F., C.L., B.H.) and State Key Laboratory of Plant Molecular Genetics and Institute of Plant Physiology and Ecology (H.L.), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China;
... fully sequenced (Fig. 2C). Only one open reading frame (ORF) was identified in
the 8.8-kb DNA fragment using FGENESH gene prediction analysis (http://linux1.
softberry.com/berry.phtml; Fig. 2D). Two BACs corresponding ...
PLoS ONE
6(8): e24230. doi:10.1371/journal.pone.0024230
Next Generation Sequencing Provides Rapid Access to the Genome of Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust
Cantu et al.,
Department of Plant Sciences, University of California Davis, Davis, California, United States of America
Genome Center, University of California Davis, Davis, California, United States of America
... 12]. Exon-intron structures of transposable elements were predicted with the aid
of Softberry FGENESH (linux1.softberry.com). Protein sequences of transposable
elements were aligned using MAFFT with the linsi option [29]. ...
J. Exp. Bot.
(2011) 62 (8): 2585-2597.
doi: 10.1093/jxb/erq433
Time course and amplitude of DNA methylation in the shoot apical meristem are critical points for bolting induction in sugar beet and bolting tolerance between genotypes
Trap-Gentil et al.,
1Universite d'Orleans, UFR-Faculte des Sciences, UPRES EA 1207 ‘Laboratoire de Biologie des Ligneux et des Grandes Cultures’ (LBLGC), rue de Chartres, BP 6759, F-45067 Orleans, France
2INRA, USC1328 Arbres et Reponses aux Contraintes Hydriques et Environnementales (ARCHE), F-45067 Orleans, France
... The determination of transposable elements (TEs) in the BvFLC and BvVIN3 genomic sequences
was realized by the identification of potential coding sequences (Fgenesh on http://linux1.softberry.
com/berry.phtml) followed by similarity analysis using BLASTP and analysis of ...
African Journal of Biotechnology
Vol. 10 (66), pp. 14738-14745, 26 October, 2011
DOI: 10.5897/AJB11.667
Isolation of candidate disease resistance genes from enrichment library of Oryza minuta based on conserved domains
Han et al.,
1State Key Laboratory of Hybrid Rice, Longping Branch of Graduate School, Central South University, Changsha 410125, P. R. China.
2China National Hybrid R&D Center, Changsha 410125, P. R. China.
... The gene prediction program used was FGENESH (http:// www.softberry.com.cn), and the
domains were predicted by the SMART program (http://smart.embl-heidelberg.de/) and CDD
program (http://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd). Results. ...
Molecular Breeding
Volume 28, Issue 3 , pp 343-357 DOI: 10.1007/s11032-010-9487-0
Identification of suitable reference genes for studying gene expression in cucumber plants subjected to abiotic stress and growth regulators
M. Migocka, A. Papierniak
1. Department of Plant Physiology, Institute of Plant Biology, Wroclaw University, Kanonia 6/8, 50-328, Wroclaw, Poland
... The selected cucumber sequences were then input into the programs identifying the full
cDNA sequences (comprising the 5? and 3? ends): GeneMark (http://exon.gatech.edu/
eukhmm.cgi) and FGENESH (http://www.softberry.ru/berry.phtml). ...
BMC Evolutionary Biology
2011, 11:165 doi:10.1186/1471-2148-11-165
Immunoglobulin heavy chains in medaka (Oryzias latipes)
Susana Magadan-Mompo 1, Christian Sanchez-Espinel 2 and Francisco Gambon-Deza 3
1 Oceanographic Center of Vigo, Spanish Institute of Oceanography (IEO), Subida a Radio Faro 50, 36390 Vigo, Pontevedra, Spain
2 Shared Unit of Immunology, University of Vigo - Vigo University Hospital Complex (Hospital Meixoeiro), Edificio de Ciencias Experimentales, Rua das Abeleiras, Campus As LagoasMarcosende, Vigo 36310, Pontevedra, Spain
... immunoglobulin mRNAs. Limits of unpublished antibodies were deduced following
instructions in the software FGENESH (http://www.softberry.com webcite) and Augustus
(http://augustus.gobics.de/submission webcite) [26]. Messenger ...
New Phytologist
189: 710–722. doi: 10.1111/j.1469-8137.2010.03492.x
Isolation and characterization of MAT genes in the symbiotic ascomycete Tuber melanosporum.
Rubini et al.,
1 National Research Council, Plant Genetics Institute – Perugia Division, Via della Madonna Alta 130, I–06128 Perugia, Italy
2 UMR 1136, Interactions Arbres/Microorganismes, INRA-Nancy, F–54280 Champenoux, France
... comparison and dotplot analysis were carried out using National Center for Biotechnology
Information (NCBI) blast and Dotmatcher (EMBOSS Package v. 6.0.1). Gene structure prediction
of MAT1-1-1 was performed with fgenesh software (http://linux1.softberry.com) using ...
Journal of Plant Biology
Volume 54, Issue 5 , pp 294-302 DOI: 10.1007/s12374-011-9166-7
Genetic Variation and Evolution of the Pi9 Blast Resistance Locus in the AA Genome Oryza Species
Liu et al.,
1. Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, Hunan, 410128, China
3. Crop Biotech Institute & Graduate School of Biotechnology, Kyung Hee University, Yongin, 446–701, South Korea
... by MEGA 4.0. Gene coding regions were predicted with GeneScan (http://genes.mit.edu/
GENSCAN.html) and Fegenesh (http://linux1.softberry.com/berry.phtml?topic=
fgenesh&group=programs&subgroup=gfind) using the Pi9 sequence as the reference. ...
Molecular Genetics and Genomics
Volume 286, Issue 1 , pp 21-36 DOI: 10.1007/s00438-011-0616-1
Mapping Fusarium wilt race 1 resistance genes in cotton by inheritance, QTL and sequencing composition
Ulloa et al.,
1. USDA-ARS, Western Integrated Cropping Systems Research Unit, 17053 N. Shafter Ave., Shafter, CA, 93263, USA
2. Department of Nematology, University of California-Riverside, Riverside, CA, 92521, USA
... for analysis. Gene predic- tion and annotation were performed with the gene predic-
tion programs Augustus (Stanke and Morgenstern 2005) and FGENESH (Softberry
Mount Kisco, NY, USA, http:// www.softberry.com). Local ...
Journal of Industrial Microbiology & Biotechnology
Volume 38, Issue 9 , pp 1211-1218 DOI: 10.1007/s10295-010-0899-y
a-Amylase activity during pullulan production and ?-amylase gene analyses of Aureobasidium pullulans
Manitchotpisit et al.,
1. Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
2. Plant Biomass Utilization Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
... CA). The mRNA sequence, amino acid sequence, initial start codon, stop codon,
and number of exons were predicted by the hidden Markov model plus protein-based
gene prediction FGENESH ? (Softberry, Inc.). Calculations ...
Tropical Plant Biology
Volume 4, Issue 3-4 , pp 217-227 DOI: 10.1007/s12042-011-9083-4
Molecular and Cytological Characterization of Centromeric Retrotransposons in a Wild Relative of Rice, Oryza granulata
Dongying Gao, Zhiyun Gong, Rod A. Wing, Jiming Jiang, Scott A. Jackson
1. Center for Applied Genetic Technologies and Institute for Plant Breeding Genetics and Genomics, University of Georgia, 111 Riverbend Rd., Athens, GA, 30602, USA
2. Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
... In order to generate the phylogenetic tree with the conserved RT domains of LTR retrotransposons,
the internal sequences from OGRetro9 and other 30 retroelements were annotated with FGENESH
(http://linux1.softberry.com/berry.phtml) and GENEMARK (http://exon.gatech ...
BMC Evolutionary Biology
2011, 11:263 doi:10.1186/1471-2148-11-263
Evolutionary view of acyl-CoA diacylglycerol acyltransferase (DGAT), a key enzyme in neutral lipid biosynthesis
Turchetto-Zolet et al.,
1 Programa de Pos-Graduacao em Genetica e Biologia Molecular, Departamento de Genetica, Universidade Federal do Rio Grande do Sul, Brazil
2 Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Brazil
... The structural organization of the DGAT genes was determined after alignment of genomic DNA
and cDNA and EST sequences. Genomic sequences were also analyzed in the FGENESH gene
structure prediction program http://www.softberry.com/ webcite[58]. ...
BMC Plant Biology
2011, 11:26 doi:10.1186/1471-2229-11-26
Identification of potential target genes for the tomato fruit-ripening regulator RIN by chromatin immunoprecipitation
Masaki Fujisawa, Toshitsugu Nakano and Yasuhiro Ito
National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
... Gene structures were predicted using the sim4 [60] and the FGENESH 2.6 [61] programs with a parameter for the tomato genome (available at the Softberry site: http://linux1.softberry.com/berry.phtml ...
Journal of Genetics and Genomics
Volume 38, Issue 7, 20 July 2011, Pages 315–325 DOI: 10.1016/j.jgg.2011.06.003
Use of methylation filtration and C0t fractionation for analysis of genome composition and comparative genomics in bread wheat
Bandopadhyay et al.,
a Department of Genetics & Plant Breeding, Ch. Charan Singh University, Meerut 250004, India
b Department of Biotechnology, Birla Institute of Technology, Mesra 835215, Ranchi, India
... Gene prediction was achieved using FGenesH (http://softberry.com/berry.phtml). 2.9.
Fluorescence in situ hybridization (FISH). Four RD clones containing SSRs were used as
probes, which were labeled with digoxigenin-11-dUTP by nick translation. ...
Theoretical and Applied Genetics
Volume 123, Issue 6 , pp 973-983 DOI: 10.1007/s00122-011-1640-6
Fine genetic mapping of cp: a recessive gene for compact (dwarf) plant architecture in cucumber, Cucumis sativus L.
Li et al.,
1. Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100, China
2. Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
... Gene annotation was performed with the computer program FGENESH (http://sunl.softberry.com/)
and function prediction was conducted with BLASTx at the NCBI (National Center for
Biotechnology Information) website (http://blast.ncbi.nlm.nih.gov). Molecular marker analysis ...
Theoretical and Applied Genetics
Volume 122, Issue 4 , pp 795-803 DOI: 10.1007/s00122-010-1487-2
Fine genetic mapping localizes cucumber scab resistance gene Ccu into an R gene cluster
Kang et al.,
1. Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
3. Key Laboratory of Horticultural Crops Genetic Improvement, Ministry of Agriculture, 100081, Beijing, China
... Gene prediction was performed with the computer program BGF (http://bgf.genomics.org.cn) and
verified by FGENESH (http://sunl.softberry.com/) (Salamov and Solovyev 2000), GENESCAN
(http://genes.mit.edu/GENSCAN.html) (Burge and Karlin 1997), TwinScan (http://mblab ...
BMC Genomics
2011, 12:609 doi:10.1186/1471-2164-12-609
Structural characterization of helitrons and their stepwise capturing of gene fragments in the maize genome
Dong et al.,
State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
... Then the obtained sequences were extended 10 kb each in the 5'-terminus and
3'-terminus respectively. Finally, the obtained putative autonomous helitrons were
annotated by Fgenesh (http://linux1.softberry.com/berry.phtml webcite). ...
Agricultural Sciences in China
Volume 10, Issue 4, April 2011, Pages 481–489 DOI: 10.1016/S1671-2927(11)60028-X
Characterization of Zm26Sub5 and Its Potential Roles in Regulating Pollen Fertility of S-CMS in Maize
Zheng-feng ZHANG a, b, Yong-lian ZHENG b
a College of Life Science, Huazhong Normal University, Wuhan 430079, P.R. China
b National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P.R. China
... embl-heidelberg.de/Alignment/). Gene prediction for the Zm26Sub5 DNA sequence
was carried out, analyzing introns, exons, and poly(A), with the FGENESH 2.6 program
(http://www.softberry.com/all/ htm). The protein encoded ...
The Plant Journal
2011, 65: 230–243. doi: 10.1111/j.1365-313X.2010.04414.x
Identification of legume RopGEF gene families and characterization of a Medicago truncatula RopGEF mediating polar growth of root hairs.
Riely et al.,
1 Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA 95616, USA
2 Beijing Forestry University, Beijing, China
...Bacterial artificial chromosomes identified as containing possible RopGEFs were analyzed using softberry fgenesh gene prediction tools to identify possible open reading frames in MtRopGEFs (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind). ...
Molecular and Cellular Biochemistry
Volume 357, Issue 1-2 , pp 263-274 DOI: 10.1007/s11010-011-0897-z
Alternative promoter usage and differential expression of multiple transcripts of mouse Prkar1a gene
Abdul Rouf Banday, Shafquat Azim, Mohammad Tabish
1. Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, Uttar Pradesh, 202002, India
... mit.edu/GENSCAN.html), GeneSplicer (http://cbcb.umd. edu/software/GeneSplicer/),
FGENESH (http://www.soft berry.com/berry.phtml). Alignment analysis was carried
out using the Gene stream Align tool (http://www2.igh.cnrs. ...
Theoretical and Applied Genetics
Volume 122, Issue 7 , pp 1247-1264 DOI: 10.1007/s00122-011-1528-5
Molecular basis of seed lipoxygenase null traits in soybean line OX948
Reinprecht et al.,
1. Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
3. Agriculture and Agri-Food Canada, Greenhouse and Processing Crops Research Centre, Harrow, ON, N0R 1G0, Canada
... 2007) during the current study. The gene structure was also analyzed with the FGenesh 2.6
available at http://www. linux1.softberry.com (Salamov and Solovyev 2000). Translation of
nucleotide sequences was generated on ExPASy (http://www.expasy.ch/tools/dna.html). ...
Plant Biotechnology Reports
Volume 5, Issue 4 , pp 331-344 DOI: 10.1007/s11816-011-0187-y
Isolation of an Rx homolog from C. annuum and the evolution of Rx genes in the Solanaceae family
Shi et al.,
1. Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
2. Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
... GENESCAN (http://genes.mit.edu/GENSCAN.html) and FGENESH (http://linux1.softberry.com/
berry.phtml) were used for BAC sequence annotation of a Rx1-containing BAC from potato, a
CapRGC-containing BAC from pepper, and a LaRGC-containing BAC from tomato. ...
New Phytologist
2011, 192: 713–726. doi: 10.1111/j.1469-8137.2011.03824.x
Conservation and clade-specific diversification of pathogen-inducible tryptophan and indole glucosinolate metabolism in Arabidopsis thaliana relatives.
Bednarek et al.,
1 Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Carl-von-Linne-Weg 10, D-50829 Koln, Germany
2 Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
... To predict the open reading frames (ORFs) from the genomic candidate regions, Fgenesh
(http://www.softberry.com) was used with parameters optimized for A. thaliana. The predicted
proteins were aligned using ClustalW and visualized using Jalview (Waterhouse et al., 2009). ...
PLoS Genet
7(4): e1002029. doi:10.1371/journal.pgen.1002029
The Phylogenetic Origin of oskar Coincided with the Origin of Maternally Provisioned Germ Plasm and Pole Cells at the Base of the Holometabola.
Lynch et al.,
Affiliation: Institute for Developmental Biology, University of Cologne, Cologne, Germany
Department of Biology, McGill University, Montreal, Canada
...The genomic region surrounding the region showing homology to Osk was used as input into FgenesH using the Apis model at http://linux1.softberry.com/ to predict an Osk sequence, ...
Mobile DNA
2011, 2:12 http://www.mobilednajournal.com/content/2/1/12
Crypton transposons: identification of new diverse families and ancient domestication events
Kenji K Kojima and Jerzy Jurka
Genetic Information Research Institute, 1925 Landings Drive, Mountain View,
CA 94043, USA
...We predicted exon-intron boundaries
with the aid of SoftBerry FGENESH:
http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind...
Genetica
Volume 139, Issue 4 , pp 489-496 DOI: 10.1007/s10709-011-9569-x
Transfer of a chromosomal Maverick to endogenous bracovirus in a parasitoid wasp
Dupuy et al.,
1. Institut de Recherche sur la Biologie de l’Insecte, UMR CNRS 6035, Universite F. Rabelais, UFR Sciences et Techniques, Parc Grandmont, 37200, Tours, France
... The hit was considered significant when the e-value was lower than 10-4. Open reading frames
(ORFs) were identified using FGENESH (http://linux1.softberry.com) and putative ORFs were
confirmed and adjusted if necessary through alignments with T. castaneum Maverick ...
Nature
478, 119–122 (06 October 2011) doi:10.1038/nature10431
Control of flowering and storage organ formation in potato by FLOWERING LOCUS T
Navarro et al.,
Departamento de Genetica Molecular de Plantas, Centro Nacional de Biotecnologia-CSIC. Calle Darwin 3, 28049 Madrid, Spain
Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0101, Japan
... The best genome matches (Supplementary Table 2)were downloaded and open reading frames were predicted using FGENESH (http://linux1.softberry.com/berry.phtml) and ORF Finder ...
BMC Evolutionary Biology
2011, 11:219 doi:10.1186/1471-2148-11-219
A survey of green plant tRNA 3'-end processing enzyme tRNase Zs, homologs of the candidate prostate cancer susceptibility protein ELAC2
Fan et al.,
1 Laboratory of Yeast Genetics and Molecular Biology, School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
2 Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
...The splicing pattern was verified using the FGENESH and FGENESH_GC programs provided at the Softberry website...
PLoS ONE
(2011) 6(8): e22046. doi:10.1371/journal.pone.0022046
Spliceosomal Intron Insertions in Genome Compacted Ray-Finned Fishes as Evident from Phylogeny of MC Receptors, Also Supported by a Few Other GPCRs.
Zhang et al.,
Department of Biology, University of Padua, Padova, Italy, Abteilung fur Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universitat zu Kiel, Kiel, Germany
...To ensure correct gene structures of all putative GPCR genes, we predicted gene structures using
GENSCAN [97], [98] and predictions were repeated using GENOMESCAN [97], [98], GENEWISE [99] and
FGENESH/FGENESH+ [31]. Intron-exon structures were determined with the aid of GENEWISE [99]
and/or PROT_MAP module of the Softberry software suite (website: www.softberry.org). ...
MPMI
Vol. 24, No. 1, 2011, pp. 79–90. doi:10.1094/ MPMI -06-10-0131
TaDAD2, a Negative Regulator of Programmed Cell Death,
Is Important for the Interaction
Between Wheat and the Stripe Rust Fungus
Wang et al.,
1
College of Plant Protection and Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University,
Yangling, Shaanxi, 712100, P. R. China; 2
College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100,
P. R. China;
...The HsDAD (Homo sapiens) was employed as the outgroup control for the construction of phylogenetic trees. Gene structure was predicted
by FGENESH....
PLoS Genet
(2011), 7(8): e1002230. doi:10.1371/journal.pgen.1002230
Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea.
Amselem et al.,
Unite de Recherche Genomique – Info, UR1164, INRA, Versailles, France, Biologie et Gestion des Risques en Agriculture – Champignons Pathogenes des Plantes, UR1290, INRA, Grignon, France
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
...For S. sclerotiorum and B. cinerea B05.10, gene structures were predicted using a combination of FGENESH and GENEID....
Molecular Ecology
(2011), 20: 2603–2618. doi: 10.1111/j.1365-294X.2011.05119.x
Characterization of a genomic divergence island between black-and-yellow and gopher Sebastes rockfishes.
BUONACCORSI et al.,
1 Juniata College, 1700 Moore St. Huntingdon, PA 16652, USA
2 Columbia River Inter-Tribal Fish Commission, 3059-F National Fish Hatchery Road, Hagerman, ID 83332, USA
... The sequenced region was manually annotated using ab initio gene predictions from
Genscan (Burge & Karlin 1997) and FgenesH (SoftBerry; Fish gene model). Microsatellites
were identified using Tandem Repeat Finder (Benson 1999). ...
Nature Biotechnology
29, 922–927 (2011) doi:10.1038/nbt.1976
Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris.
Berka et al.,
Novozymes, Inc., Davis, California, USA.
US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada.
... was performed using ab initio Fgenesh 32 and Genemark-ES 33 ; homology-based Fgenesh+ 32 and
Genewise 34 seeded by BLASTx alignments of NCBI's nr (nonredundant) protein database against the assembly;
cDNA-based EST_map (http://www.softberry.com/) seeded ...
Plant Physiology
October 2011 vol. 157 no. 2 937-946 DOI: 10.1104/pp.111.174912
Evolution of the S-Locus Region in Arabidopsis Relatives
Ya-Long Guo 2*, Xuan Zhao 2, Christa Lanz and Detlef Weigel
Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
... Annotation of the BAC sequences was performed using FGENESH (http://linux1.
softberry.com/berry.phtml). The annotation was confirmed by ...
Nature Communications
2, Article number: 202 doi:10.1038/ncomms1189
Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations
Rouxel et al.,
INRA-Bioger, UR1290, Avenue Lucien Bretignieres, BP 01, Thiverval-Grignon F-78850, France.
Murdoch University, South Street, Murdoch, Western Australia 6150, Australia.
...The EuGene prediction pipeline v. 3.5a (ref. 48), which integrates ab initio (Eugene_IMM, SpliceMachine and Fgenesh 2.6 (www.softberry.com)) and similarity methods (BLASTn, GenomeThreader, BLASTx), was used to predict gene models. ...
Nature Genetics
43, 228–235 (2011) doi:10.1038/ng.769
The draft genome of the parasitic nematode Trichinella spiralis
Mitreva et al.,
The Genome Center, Washington University School of Medicine, St. Louis, Missouri, USA.
Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA.
...Protein-coding genes were predicted using a combination of ab initio programs47 and FgenesH (Softberry, Corp) and the evidence-based program EAnnot48. ...
Theoretical and Applied Genetics
Volume 122, Issue 3 , pp 459-470 DOI: 10.1007/s00122-010-1460-0
Characterization and genetic analysis of a low-temperature-sensitive mutant, sy-2, in Capsicum chinense
An et al.,
1. Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul, 151-921, Korea
2. Key Laboratory of Crop Genomics and Genetic Improvement of Ministry of Agriculture, Beijing Key Lab of Crop Genetic Improvement, China Agriculture University, Beijing, 100094, China
... C2_At1g09070. In the sequence, 51 genes were predicted by gene prediction
FGENESH (http://linux1.softberry. com) and blastx (http://blast.ncbi.nlm.nih.gov). There
were several candidate genes including five lipoxygenase genes, ...
The Plant Journal
(2011), 65: 745–756. doi: 10.1111/j.1365-313X.2010.04461.x
Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution.
Quraishi et al.,
1 INRA/Universite Blaise Pascal UMR 1095 GDEC, Domaine de Crouelle, 234 Avenue du Brezet, 63100 Clermont-Ferrand, France
2 BIOGEMMA, 8 Rue des Freres Lumiere, 63028 Clermont-Ferrand Cedex 2, France
... nih.gov/) and SwissProt databases (http://expasy.org/sprot/), with the results of two gene predictor
programs, Eugene (Matheet al., 2002) with the rice (Oryza sativa) training version and FgeneSH
(Salamov and Solovyev, 2000) with default parameters (http://sun1.softberry.com/). ...
Plant Physiology October
2011 vol. 157 no. 2 757-769 DOI: 10.1104/pp.111.181990
Genome-Wide Comparison of Nucleotide-Binding Site-Leucine-Rich Repeat-Encoding Genes in Arabidopsis
Guo et al.,
Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
... Gordon et al., 1998). Primer walking and PCR were used to fill or polish gaps and
ambiguous regions. Annotation was performed using FGENESH and FGENESH+
(http://linux1.softberry.com/berry.phtml). Spidey (http://www.ncbi ...
BMC Genomics
2011, 12:142 doi:10.1186/1471-2164-12-142
Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis
Tian et al.,
1 Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
2 Arizona Genomics Institute, The University of Arizona, Tucson, AZ 85721, USA
... Putative gene models were predicted using the FGENESH program with the monocot training
set (http://www.softberry.com webcite), and were further investigated to determine whether they
are actually genes following described previously criteria [6]. Truncated gene fragments ...
The Plant Journal
(2011), 68: 777–787. doi: 10.1111/j.1365-313X.2011.04728.x
Rice 14-3-3 protein (GF14e) negatively affects cell death and disease resistance.
Manosalva, P. M., Bruce, M. and Leach, J. E.
Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.
... Throughput Genomic Sequences (HTGS) database. The fgenesh program
(http://www.softberry.com/berry.phtml) was used to predict 14-3-3 gene members
from significant rice BAC hits. All sequences corresponding to various ...
Genomics
Volume 97, Issue 5, May 2011, Pages 313–320 DOI: 10.1016/j.ygeno.2011.02.007
Comparative analysis of Gossypium and Vitis genomes indicates genome duplication specific to the Gossypium lineage
Lin et al.,
a Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605, USA
b Center for Genomics and Biocomputing, College of Sciences, Hebei Polytechnic University, Tangshan, Hebei, 063000, China
...Genes were identified from BAC sequences using FGENESH (http://linux1.softberry.com/berry.phtml). ...
BMC Evolutionary Biology
2011, 11:78 doi:10.1186/1471-2148-11-78
Evolution of Parallel Spindles Like genes in plants and highlight of unique domain architecture
Cigliano et al.,
1 CNR - National Research Council of Italy, Institute of Plant Genetics, Research Division Portici, Via Universita 133, 80055 Portici. Italy
2 DISSPAPA, Dept. of Soil, Plant and Environmental Sciences, University of Naples "Federico II", Via Universita 100, 80055 Portici. Italy
... Germany). PSL1 gene structure and cDNA predictions were carried out using FGENESH
online tool (http:/ / linux1.softberry.com/ berry.phtml?topic=fgenesh&group=pro
grams&subgroup=gfind webcite) selecting Tomato as organism. ...
BMC Research Notes
2011, 4:518 doi:10.1186/1756-0500-4-518
Identification of superior reference genes for data normalisation of expression studies via quantitative PCR in hybrid roses (Rosa hybrida)
Maik Klie and Thomas Debener
Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universitat Hannover, Herrenhauser Str. 2, 30419 Hannover, Germany
...Open reading frames and 5'and 3' UTR regions were predicted using the
FGENESH algorithm [34] with specifications for dicot plants....
Aging Cell
(2011), 10: 896–907. doi: 10.1111/j.1474-9726.2011.00727.x
Alternative splicing factor or splicing factor-2 plays a key role in intron retention of the endoglin gene during endothelial senescence.
Blanco, F. J. and Bernabeu, C.
Centro de Investigaciones Biologicas, Consejo Superior de Investigaciones Cientificas (CSIC), and Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), c/Ramiro de Maeztu 9, 28040 Madrid, Spain
... Genome Bioinformatics (http://genome.ucsc.edu/). Then, the FSPLICE and FGENESH
tools were used to predict exons and introns in the DNA sequences (http://linux1.
softberry.com/berry.phtml). The Transeq tool at the European ...
PLoS Pathog
(2011), 7(7): e1002137. doi:10.1371/journal.ppat.1002137
Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens.
Klosterman et al.,
USDA-ARS, Salinas, California, United States of America
University of California, Davis, California, United States of America
...Protein-encoding genes were annotated using a combination of manually curated genes, in addition to EST BLAST alignments, and ab initio gene predictions
made by FGENESH, FGENESH+ (http://linux1.softberry.com), and ...
PLoS Negl Trop Dis
(2011), 5(10): e1340. doi:10.1371/journal.pntd.0001340
Characterisation of the Trichinella spiralis Deubiquitinating Enzyme, TsUCH37, an Evolutionarily Conserved Proteasome Interaction Partner.
White et al.,
Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, London, United Kingdom
Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
...Contig 1.2 was analysed by 4 different gene prediction programmes: AUGUSTUS [24], GenemarkHMM [31], SNAP [32]
and Fgenesh [33]. ...
The Plant Cell May
2011 vol. 23 no. 5 1861-1875 DOI: 10.?1105/?tpc.?111.?085456
A Small Zinc Finger Thylakoid Protein Plays a Role in Maintenance of Photosystem II in Arabidopsis thaliana
Yan Lu a, 1, David A. Hall a and Robert L. Last a,b,2
aDepartment of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
bDepartment of Plant Biology, Michigan State University, East Lansing, Michigan 48824
...Complete genomic sequence (including 500 bp upstream and downstream of the original partial sequence) was used to predict new gene structures with the
FGENESH program (a Hidden Markov Model-based gene prediction program; http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind)....
PLoS ONE
(2011), 6(3): e17505. doi:10.1371/journal.pone.0017505
Elucidation of Functional Markers from Aspergillus nidulans Developmental Regulator FlbB and Their Phylogenetic Distribution.
Cortese MS, Etxebeste O, Garzia A, Espeso EA, Ugalde U
Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country, San Sebastian, Spain, IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
Department of Cellular and Molecular Medicine, Centro de Investigaciones Biologicas (CSIC), Madrid, Spain
...and Fgenesh (Softberry) [71] were considered along with manual verification of splice sites....
Genome Biology
2011, 12:R48 doi:10.1186/gb-2011-12-5-r48
A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure
Zuccolo et al.,
1 Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, AZ 85721, USA
2 Department of Plant Biology, University of Georgia, 4504 Miller Plant Sciences, Athens, GA 30602, USA
...FGENESH [63] annotations for the Amborella contigs were included on the horizontal axes of the dot plots. ...
Plant Physiology
October 2011 vol. 157 no. 2 770-789 DOI: 10.?1104/?pp.?111.?179648
The Tomato Terpene Synthase Gene Family
Falara et al.,
Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109–1048 (V.F., T.A.A., T.T.H.N., I.S., Y.M., M.E.B., E.P.); Department of Plant Physiology, Swammerdam Institute of Life Sciences, 1098 XH Amsterdam, The Netherlands (E.A.S., P.M.B., R.C.S.)
...he FGENESH gene prediction tool (www.softberry.com) was used for initial annotation of the predicted tomato TPS genes....
PLoS Pathog
(2011), 7(11): e1002348. doi:10.1371/journal.ppat.1002348
Multiple Candidate Effectors from the Oomycete Pathogen Hyaloperonospora arabidopsidis Suppress Host Plant Immunity. PLoS Pathog 7(11): e1002348. doi:10.1371/journal.ppat.1002348
Fabro et al.,
The Sainsbury Laboratory, John Innes Centre, Norwich, United Kingdom
School of Life Sciences, Warwick University, Wellesbourne, United Kingdom
...ORFs from ATG to Stop codon were identified using FgenesH (www.softberry.com) and ...
BMC Plant Biology
2011, 11:20 doi:10.1186/1471-2229-11-20
ZINC-INDUCED FACILITATOR-LIKE family in plants: lineage-specific expansion in monocotyledons and conserved genomic and expression features among rice (Oryza sativa) paralogs
Ricachenevsky et al.,
1 Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Goncalves 9500, P.O.Box 15005, Porto Alegre, 91501-970, Brazil
2 Departamento de Botanica, Instituto de Biociencias, Universidade Federal do Rio Grande do Sul, Av. Bento Goncalves 9500, Porto Alegre, 91501-970, Brazil
...Two unnanotated ZIFL genes from Zea mays were predicted using Fgenesh (http://www.softberry.com ...
Cytogenet Genome Res
2011;132:55-63 (DOI: 10.1159/000319491)
Sequence of a Turkey BAC Clone Identifies MHC Class III Orthologs and Supports Ancient Origins of Immunological Gene Clusters
L.D. Chaves a, b, S.B. Krueth a, M.M. Bauer a, K.M. Reed a
aDepartment of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minn., and
bNational Jewish Health, Division of Allergy and Clinical Immunology, Department of Medicine, Denver, Colo., USA
... Sequences were analyzed with the basic local alignment search tool (BLAST), GENESCAN
(http://genes.mit.edu/GENSCAN.html) and Softberry FGENESH (http://linux1.softberry.com/
all.htm) to identify putative transcripts and homologies to known genes. ...
Gene
Volume 452, Issue 2, 1 March 2010, Pages 45-53, doi:10.1016/j.gene.2009.11.001
Comparative genomics identifies new alpha class genes within the avian glutathione S-transferase gene cluster
Ji Eun Kim a, Miranda M. Bauer b, Kristelle M. Mendoza b, Kent M. Reed b and Roger A. Coulombe Jr. a,
a Department of Veterinary Sciences and Graduate Toxicology Program, Utah State University, Logan, UT 84322, USA
b Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN 55108, USA
.. 2.4. Gene identification and annotation. The assembled sequence was analyzed with Softberry
FGENESH (http://linux1.softberry.com/all.htm) and the basic local alignment search tool (BLAST)
to identify putative transcripts and homologies to known genes. ...
Gene
Volume 468, Issues 1-2, 15 November 2010, Pages 41-47 doi:10.1016/j.gene.2010.08.003
Two conserved Z9-octadecanoic acid desaturases in the red flour beetle, Tribolium castaneum
Irene Horne a, Nerida Gibb a, Katherine Damcevski a, Karen Glovera and Victoria S. Haritos a
a CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601, Australia
... were obtained. Each of the contigs was then subjected to a gene prediction program
in Softberry (http://www.softberry.com/cgi- bin/programs/gfin/fgenesh) using
parameters for Brugia malaya and Caenorhabditis elegans. 2.2 ...
Journal of Invertebrate Pathology
Volume 105, Issue 2, October 2010, Pages 156-163 doi:10.1016/j.jip.2010.06.003
Transient transcription of a putative RNase containing BEN domain encoded in Cotesia plutellae bracovirus induces an immunosuppression of the diamondback moth, Plutella xylostella
Bokri Park and Yonggyun Kim
Department of Bioresource Sciences, Andong National University, Andong 760-749, Republic of Korea
... 17 18 2.2. Gene prediction using bioinformatic tools 19 20 Open reading frame (ORF) was
predicted from a viral genome segment using 21 FGENESH program (Softberry, Inc., Mount Kisco,
NY, USA) by access to 22 http://linux1.softberry.com/berry.phtml?topic=index&group ...
Genome
Volume 53, Number 1, 1 January 2010 , pp. 55-67(13)
Microsatellites in Brassica unigenes: relative abundance, marker design, and use in comparative physical mapping and genome analysis
Parida, Swarup K.; Yadava, Devendra K.; Mohapatra, Trilochan
... Also, unigenes were checked using software tools such as FGENESH (Softberry,
Inc., Mount Kisco, New York; www. softberry.com),
ORF Finder (Stothard 2000; http://
bioinformatics.org/sms/orf_find.html), and UTRScan (http ...
Bioinformatics
2010, 26 (12): 1488-1492. doi: 10.1093/bioinformatics/btq167
Ergatis: a web interface and scalable software system for bioinformatics workflows
Orvis et al.,
1 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 2 J. Craig Venter Institute, Rockville, MD, USA
... Ergatis contains components for over a dozen different gene prediction programs, such as
GeneWise (Birney et al., 2004), GeneMark (Besemer and Borodovsky, 2005) and FGENESH
(SoftBerry), as well as RNA prediction. ... SoftBerry. "Gene finding in Eukaryota.". ...
Mol Biol Evol
2010, 27 (11): 2487-2506. doi: 10.1093/molbev/msq133
Orthologous Comparisons of the Hd1 Region across Genera Reveal Hd1 Gene Lability within Diploid Oryza Species and Disruptions to Microsynteny in Sorghum
Sanyal et al.,
1Department of Agronomy, Purdue University
2Department of Plant Sciences, BIO5 Institute, Arizona Genomics Institute, University of Arizona, Tucson
... The sequences were then annotated for genes using a combination of ab initio prediction
programs FGENESH (www.softberry.com, Salamov and Solovyev 2000) and Page 8. 8 ...
(www.softberry.com, Salamov and Solovyev 2000) and with previous annotation. We ...
Nucl. Acids Res
2010 doi: 10.1093/nar/gkq1016
FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum
Wong et al.,
1Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology, Ingolstadter Landstrasse 1, D-85764 Neuherberg, 2Max-Planck-Institute for Terrestrial Microbiology, Department of Organismic Interactions, D-35043 Marburg,
... Based on this set, all gene loci in FGDB v3.1 were re-annotated using a pipeline including (i)
Fgenesh with different matrices (www.softberry.com); (ii) GeneMark-ES (8); (iii) Augustus with
ESTs, precedingly annotated Fusarium models and/or Neurospora crassa protein ...
PLoS ONE
5(3): e9620. doi:10.1371/journal.pone.0009620
Morphological and Genomic Characterization of Filobasidiella depauperata: A Homothallic Sibling Species of the Pathogenic Cryptococcus Species Complex
Marianela Rodriguez-Carres, Keisha Findley, Sheng Sun, Fred S. Dietrich, Joseph Heitman
Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
... Assembled sequences were subsequently annotated employing the gene predictor software
FGENESH from SoftBerry© and using as reference current gene predictions in C. neoformans
(http://linux1.softberry.com/berry.phtml??topic=fgenesh&group=programs&subgroup=gf ...
Mol Biol Rep.
2010 Feb;37(2):801-8. Epub 2009 Jul 4
Molecular cloning and characterization of five genes encoding pentatricopeptide repeat proteins from Upland cotton (Gossypium hirsutum L.)
Yang L, Zhu H, Guo W, Zhang T
National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.
... The remaining non- redundant sequences were assembled by CAP3 assembly tool [24] with
default parameter. Potential genes of BAC sequences originated from the G. hirsutum database
were predicted by a program: FGENESH (http://www.softberry. ...
J Mol Evol.
2010 Jan 1. [Epub ahead of print]
Strong Positive Selection Drives Rapid Diversification of R-Genes in Arabidopsis Relatives
Chen Q, Han Z, Jiang H, Tian D, Yang S.
State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China.
... the gene-finding programs FGENESH (http://www. softberry.com/) and GENSCAN
(http://genes.mit.edu/ genescan.html/) to obtain information on complete open reading
frames. To exclude potentially redundant candidate NBS ...
Eukaryotic Cell
January 2010, p. 164-172, Vol. 9, No. 1 doi:10.1128/EC.00194-09
Evolutionary Dynamics of Mating-Type Loci of Mycosphaerella spp. Occurring on Banana
Mahdi Arzanlou, 1,2,3 Pedro W. Crous, 1,2 and Lute-Harm Zwiers 1
Evolutionary Phytopathology, CBS-KNAW Fungal Biodiversity Center, Utrecht 3508 AD, The Netherlands,1 Wageningen University and Research Center (WUR), Laboratory of Phytopathology, Wageningen 6708 PB, The Netherlands,2
... reading frames (ORFs) and intron positions were predicted by comparing the sequence data
with known MAT sequences from other filamentous fungi, as well as by means of the FGENESH
gene prediction module from the MOLQUEST software package (Softberry, Inc., Mount ...
Plant Molecular Biology Reporter
Volume 28, Number 1, March 2010 , pp. 152-161(10) DOI: 10.1007/s11105-009-0134-z
Identification of NBS-Type Resistance Gene Homologs in Tobacco Genome
Xiaodong et al.,
1: Institute of Crop Science, Zhejiang University, Hangzhou, 310029, China 2: Joint Laboratory of Tobacco Bioinformatics, Yunnan Institute of Tobacco Science, Yuxi, 653100, China,
... 2006) for sequence cleaning and assembly. FGENESH was used to perform gene prediction
(http://www.softberry.com) (Salamov and Solovyev 2000). HMMER (Eddy 1998) was used to
search protein sequences Plant Mol Biol Rep (2010) 28:152–161 153 Page 3. ...
J. Agric. Food Chem.
2010, 58 (5), pp 3184–3190
DOI: 10.1021/jf904367r
An Acidophilic and Acid-Stable b-Mannanase from Phialophora sp. P13 with High Mannan Hydrolysis Activity under Simulated Gastric Conditions
Zhao et al.,
Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
... sequence. Sequence Analysis The exon-intron structure of the full-length mannanase
gene was predicted using GENESCAN (http://genes.mit.edu/GENSCAN.html) and
FGENESH (http://www.softberry.com/berry.phtml/). The ...
New Phytologist
Special Issue: Plant polyploidy
Volume 186, Issue 1, pages 228–238, April 2010 DOI: 10.1111/j.1469-8137.2009.03164.x
Tandem duplication of the FLC locus and the origin of a new gene in Arabidopsis related species and their functional implications in allopolyploids
Nah, G. and Jeffrey Chen, Z.
1. Section of Molecular Cell and Developmental Biology
2. Institute for Cellular and Molecular Biology
3. Section of Integrative Biology
4. Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA
... Sonnhammer & Durbin, 1995). The genomic sequences were annotated using fgenesh
(http://www.softberry.com), a gene prediction software program for A. thaliana genome
annotation (Swarbreck et al., 2008). The predicted genes ...
Funct Integr Genomics.
2010 May;10(2):241-51. Epub 2009 Dec 12
Recruitment of closely linked genes for divergent functions: the seed storage protein (Glu-3) and powdery mildew (Pm3) genes in wheat (Triticum aestivum L.)
Wang ZN, Huang XQ, Cloutier S.
Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, MB, Canada, R3T 2M9.
... ricegaas.dna.affrc. go.jp/) using the gene prediction algorithm of FGENESH Funct
Integr Genomics Page 3. (http://www.softberry.com/) and GENESCAN (http://gene
mark.mit.edu/GENESCAN.htm). The predicted gene sequences ...
Journal of Basic Microbiology
Volume 50, Issue 1, pages 59–71, February 2010 DOI: 10.1002/jobm.200900113
Adenylyl cyclase regulates heavy metal sensitivity, bikaverin production and plant tissue colonization in Fusarium proliferatum
Gabor Kohut 1,
Brigitta Olah 1,
Attila L. Adam 1,
Jorge Garcia-Martinez 2,
Laszlo Hornok Prof. 1
1. Agricultural Biotechnology Center, Mycology Group of the Hungarian Academy of Sciences, Institute of Plant Protection, Szent Istvan University, Godollo, Hungary
2. Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain
... Biotechnology Centre (Godollo, Hungary). Se- quence data were analyzed with the
Lasergene software package (DNAStar Inc., Madison, Wisconsin, USA) and the
FGENESH program (http://www.softberry.com). Blast searches were ...
Theor Appl Genet.
2010 Apr;120(6):1099-106. Epub 2009 Dec 24
Fine mapping of pepper trichome locus 1 controlling trichome formation in Capsicum annuum L. CM334.
Kim et al.,
Department of Plant Sciences, Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, South Korea.
... 2003). Repeat sequences were filtered by RepeatMasker (http://www. repeatmasker.org)
and JDotter (http://athena.bioc.uvic.ca). The gene coding regions were predicted by
FGENESH (http://linux1.softberry.com) or GENESCAN (http://genes. ...
Eukaryotic Cell
January 2010, p. 46-58, Vol. 9, No. 1 doi:10.1128/EC.00259-09
Organization and Evolutionary Trajectory of the Mating Type (MAT) Locus in Dermatophyte and Dimorphic Fungal Pathogens
Wenjun Li, 1 Banu Metin, 1 Theodore C. White ,2 and Joseph Heitman 1
Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina,1 Seattle Biomedical Research Institute, Seattle, Washington2
... Putative genes in the MAT locus and flanking regions were predicted by using a combination
of primary annotation from the Broad Institute, GeneMark (37), BLAST (1), ORF Finder
(http://www.ncbi.nlm.nih.gov/projects/gorf/), and FGENESH (http://linux1.softberry.com/berry.phtml ...
Molecular Plant Pathology
2010, 11: 395–407. doi: 10.1111/j.1364-3703.2010.00612.x
The two-component histidine kinase Fhk1 controls stress adaptation and virulence of Fusarium oxysporum
RISPAIL, N. and DI PIETRO, A
Departamento de Genetica, Universidad de Cordoba, Campus de Rabanales Edificio Gregor Mendel C5, 14071 Cordoba, Spain
... ing the complete fhk1 gene, including the promoter, coding region and terminator, was sequenced
manually, revealing an open reading frame of 3882 bp interrupted by five putative introns,
according to the Fgenesh 2.6 prediction server (http:// linux1.softberry.com/berry.phtml ...
Funct Integr Genomics
2010 Mar;10(1):111-22. Epub 2009 Aug 2
Conserved globulin gene across eight grass genomes identify fundamental units of the loci encoding seed storage proteins
Gu YQ, Wanjugi H, Coleman-Derr D, Kong X, Anderson OD.
Western Regional Research Center, United States Department of Agricultural-Agricultural Research Service, Albany, CA 94710, USA. yong.gu@ars.usda.gov
... 2003) and wheat A genome (BAC AY494981 and DQ537335, Gu et al. 2004, 2006,
respectively). FGENESH (http://www.softberry.com/nucleo.html) and GEN- ESCAN
(http://genemark.mit.edu/GENESCAN.htm) were used for gene prediction. ...
Molecular Breeding
Volume 26, Number 2, August 2010 , pp. 275-292(18)
Genic markers for wild abortive (WA) cytoplasm based male sterility and its fertility restoration in rice
Ngangkham, Umakanta et al.,
1: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India 2: Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India
... msu.edu/pseudomolecules) and indica cultivar 93–11 (Beijing Rice Information System,
http://rice.genomics. org.cn/rice) were downloaded and annotated using FGENESH
(http://sun1.softberry.com/berry.phtml) gene prediction software to identify protein encoding genes. ...
Experimental Parasitology
Volume 127, Issue 1, January 2011, Pages 184-194 doi:10.1016/j.exppara.2010.07.012
Identification of papain-like cysteine proteases from the bovine piroplasm Babesia bigemina and evolutionary relationship of piroplasms C1 family of cysteine proteases
ATiago M. Martins a, b, Virgilio E. do Rosario b and Ana Domingos a, b
Unidade de Tecnologias de Proteinas e Anticorpos Monoclonais, Instituto de Higiene e Medicina Tropical, Estrada do Paco do Lumiar 22, 1649-038 Lisboa, Portugal
b Centro de Malaria e Doencas Tropicais, Instituto de Higiene e Medicina Tropical, Rua da Junqueira 96, 1349-008 Lisboa, Portugal
... A threshold of E 1e-04 was adopted for 93 the tblastn search (Wu et al., 2003). The gene
structure of the identified CP genes with 94 multiple exons was predicted using the
FGENESH and FGENESH+ software 95 (http://www.softberry.com). ...
Mol Genet Genomics.
2010 May;283(5):427-38. Epub 2010 Mar 9
Unique evolutionary pattern of numbers of gramineous NBS-LRR genes
Li et al.,
State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China.
... with Xanking regions of 5,000–10,000 bp on both sides, were annotated using the gene-finding
programs FGENESH with the monocot training set (http://www.soft- berry.com/) and GENSCAN
with the maize training set (http://genes.mit.edu/GENSCAN.html) to obtain informa ...
Mol Biol Evol
2010 doi: 10.1093/molbev/msq156
Tracing the evolution of the floral homeotic B- and C-function genes through genome synteny
Barry Causier *,1,
Rosa Castillo 2,4,
Yongbiao Xue 3,
Zsuzsanna Schwarz-Sommer 2 and
Brendan Davies 1
1 Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
2 Max-Planck-Institut fur Zuchtungsforschung, Carl-von-Linne-Weg 10, 50829 Koln, Germany
... Lukashin and Borodovsky 1998) (each using the Arabidopsis dataset, with default settings),
and FGENESH (www.softberry.com) (using both Arabidopsis and tobacco datasets, with
default settings). In most cases each algorithm predicted a similar ...
Veterinary Immunology and Immunopathology
Volume 137, Issues 1-2, 15 September 2010, Pages 176-180 doi:10.1016/j.vetimm.2010.04.018
Polymorphism of sheep MHC Class IIb gene TAPASIN
N. Siva Subramaniam a, E.F. Morgan a, C.Y. Lee a, J.D. Wetherall a and D.M. Groth a
Western Australian Biomedical Research Institute (WABRI) & Centre for Health Innovation Research Institute, School of Biomedical Sciences, Curtin University of Technology, Perth, Western Australia 6845, Australia
... A consensus genetic structure for sheep 108 TAPASIN was determined from analysis of the
predictions from GENSCAN (Burge & 109 Karlin 1997) Burge and Karlin, 1997), TWINSCAN
(Korf et al. 2001) and 110 FGENESH (http://www.softberry.com). ...
Theor Appl Genet.
2010 Feb;120(4):709-20. Epub 2009 Nov 3.
Nucleotide diversity and molecular evolution of the PSY1 gene in Zea mays compared to some other grass species
Fu et al.,
National Maize Improvement Center of China, Key Laboratory of Crop Genomics and Genetic Improvement, China Agricultural University, Yuanmingyuan West Road, Haidian, Beijing, China.
... Gene structure was predicted separately for each species using the soft- ware packages
FGENESH (http://linuxl.softberry.com) and NNPP (http://www.fruitfly.org). Alignments were per-
formed among all species with the ClustalX version 8.1 (Thompson et al. ...
The Journal of Immunology
May 1, 2010 vol. 184 no. 9 5038-5046 doi: 10.4049/?jimmunol.0903374
Intron-Containing Type I and Type III IFN Coexist in Amphibians: Refuting the Concept That a Retroposition Event Gave Rise to Type I IFNs
1. Zhitao Qi*†, Pin Nie*, Chris J. Secombes‡ and Jun Zou‡
*State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei;
†Chemical and Biological Engineering College, Yancheng Institute of Technology, Jiangsu, China
... ca.expasy.org/tools). Putative transcripts were predicted from the genome sequences
using the GenScan program (http://genes/mit.edu/GENSCAN.html) and the Fgenesh
program (www.softberry.com). Signal peptides were ...
Molecular Breeding
Volume 26, Number 2, August 2010 , pp. 325-338(14)
SNP haplotypes of the BADH1 gene and their association with aroma in rice (Oryza sativa L.)
Singh, Anuradha et al.,
1: Rice Genome Laboratory, National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India 2: Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India
... work well. The position of exons and introns were identified using gene prediction
software FGENESH (www.softberry.com) and verified manually by checking against
the full length cDNA sequence of the BADH1 gene. The ...
Theor Appl Genet.
2010 May;120(7):1443-50. Epub 2010 Jan 2010
Fine mapping of a resistance gene to bacterial leaf pustule in soybean
Kim DH, Kim KH, Van K, Kim MY, Lee SH
Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
... Composite interval mapping (CIM) was performed by Qgene V. 4.2.2 (Joehanes and Nelson
2008) with scan interval 1. Gene annotation was conducted with gene prediction program
FGENESH (http:// www.softberry.ru) against Arabidopsis database. ...
Plant Science
Volume 179, Issue 4, October 2010, Pages 399-406 doi:10.1016/j.plantsci.2010.06.017
Disease resistance signature of the leucine-rich repeat receptor-like kinase genes in four plant species
Tang et al.,
a State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210093 Nanjing, China
b Department of Life Science, Lianyungang Teacher's College, 222006 Lianyungang, China
... Then the nucleotide sequences of candidate Ser/Thr/Tyr kinase genes, together with flanking
regions of 5,000-10,000 bp at both sides, were annotated using the gene-finding programs
FGENESH (http://www.softberry.com/) and GENSCAN (http://genes.mit.edu/genescan.html ...
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics
Volume 5, Issue 2, June 2010, Pages 151-156 doi:10.1016/j.cbd.2010.03.006
Novel isoform of the Xenopus tropicalis PKA catalytic alpha subunit: An example of alternative splicing
Mohammad Tabish, Vladimir I. Rodionov
Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, Connecticut 06032, USA
... Gene/Exon finding tools were used at HMMgene (http://www.cbs.dtu.dk/services/HMMgene),
Genescan (http://genes.mit.edu/ GENSCAN.html), GeneSplicer (http://cbcb.umd.edu/
software/GeneSplicer/), FGENESH (http://www.softberry.com/berry.phtml). ...
Molecular breeding
2010, vol. 25, no2, pp. 187-201
Development and evaluation of broadly applicable markers for Restorer-of-fertility in pepper
Deuk et al.,
(1) Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, 151-921, Seoul, Korea
(2) Breeding and Research Station, Monsanto Korea, 363-955, Chungwon, Korea
... search using petunia Rf gene sequence as query. FGENESH program
(www.softberry.com) was used to predict gene sequences from sequences of
selected BAC clones. Among predicted fifteen genes, sequence of the first ...
Plant Science
Volume 179, Issue 3, September 2010, Pages 257-266 doi:10.1016/j.plantsci.2010.05.012
Distribution and diversity of PIF-like transposable elements in the Bambusoideae subfamily
Ming-Bing Zhou a, Jiang-Jie Lu a, Hao Zhonga, Xiang-Min Liu a and Ding-Qin Tang a
a The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, LinAn 311300, Zhejiang Province, PR China
.. The putative coding exons of these sequences, as well as those derived from our 114 PCR
experiments, were predicted using web software of Netgene2 115 (http://www.cbs.dtu.dk/services/
NetGene2/) and FGENESH 116 (http://sun1.softberry.com/berry.phtml?topic ...
Genome
Volume 53, Number 9, 1 September 2010 , pp. 658-666(9)
Comparative genomic analysis of the false killer whale (Pseudorca crassidens) LMBR1 locus
Dae-Won Kim et al.,
.. submit.html) (Benson 1999). We also searched for potential genes on the contig sequences
using FGENESH (SoftBerry, Inc., Mount Kisco, New York), geneid (http://genome.imim.
es/geneid.html), and GeneMark (http://exon.biology.gatech. edu/eukhmm.cgi). ...
Fungal Genetics and Biology
Volume 47, Issue 8, August 2010, Pages 663-671 doi:10.1016/j.fgb.2010.04.008
Phytophthora nicotianae transformants lacking dynein light chain 1 produce non-flagellate zoospores
Reena D. Narayan a, Leila M. Blackman a, Weixing Shan 1, a and Adrienne R. Hardham a
a Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
... DNA sequences were 22 searched for introns using FGENESH 23 (http://linux1.softberry.com/
berry.phtml?topic=fgenesh&group=programs&subgroup24 =gfind). For phylogenetic analysis,
homologues of DLC1 were retrieved from NCBI 25 and JGI databases. ...
Plant Physiology Preview
Published on September 10, 2010; 10.1104/pp.110.163923
Genome structures and halophyte-specific gene expression of the extremophile Thellungiella parvula in comparison to Thellungiella salsuginea (T. halophila) and Arabidopsis thaliana
Oh et al.,
1 University of Illinois Urbana-Champaign; 2 Purdue University
... An ab-initio ORF prediction with FGENESH(http://linux1.softberry.com/berry.phtml) identified 2,229
ORFs, ... The open reading frames (ORFs) in genomic sequences were predicted ab initio with
FGENESH (http://www.softberry.com) adopting Arabidopsis parameters. ...
BMC Plant Biol.
2010 Aug 19;10:183. doi:10.1186/1471-2229-10-183
Medicago truncatula contains a second gene encoding a plastid located glutamine synthetase exclusively expressed in developing seeds
Seabra AR, Vieira CP, Cullimore JV, Carvalho HG.
Instituto de Biologia Molecular e Celular da Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal.
... resources (http://www.medicago.org/genome/). Organization of both GS2 genes and prediction
of MtGS2b coding sequence was carried out using the FGENESH2.6 software from Softberry
(www.softberry.com). MtGS2a and MtGS2b amino acid sequences were ...
PLoS ONE
2010 5(4): e9958. doi:10.1371/journal.pone.0009958
Association and Linkage Analysis of Aluminum Tolerance Genes in Maize
Krill AM, Kirst M, Kochian LV, Buckler ES, Hoekenga OA
1 United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, United States of America, 2 Cornell University, Department of Plant Breeding and Genetics, Ithaca, New York, United States of America
.. Genes of interest were placed on the physical-genetic map of maize using the BLAST tool
implemented by the Maize Genome Sequencing Project [42]. Gene architecture predictions were
made using the FGenesH tool as implemented by Softberry [46]. Statistical tests. ...
Fish & Shellfish Immunology
Volume 29, Issue 4, October 2010, Pages 594-599 doi:10.1016/j.fsi.2010.06.004
Ig heavy chain genes and their locus in grass carp Ctenopharyngodon idella
Xiao et al.,
a State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, China
b Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
... sequence. The software GENSCAN (http://genes.mit.edu/GENSCAN.html), 131
FGENESH (http://linux1.softberry.com/all.htm) and BLASTX 132 (http://blast.ncbi.
nlm.nih.gov/Blast.cgi) were employed for the genome annotation. ...
Molecular breeding
2010, vol. 25, no1, pp. 155-166
Identification of major quantitative trait loci qSBR11-1 for sheath blight resistance in rice
Channamallikarjuna et al.,
(1) National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, 110012, New Delhi, India
(2) Directorate of Rice Research, Andhra Pradesh, Hyderabad, India
... Nipponbare (www.ncbi.nlm.nih.gov) was used for gene prediction. FGENESH gene pre- diction
software (www.softberry.com) was used to predict genes in this sequence. Predicted genes were
functionally annotated by using BLASTp (bit- score C 100, E value B -20) software. ...
Fungal Genetics and Biology
Volume 47, Issue 9, September 2010, Pages 761-772 doi:10.1016/j.fgb.2010.06.001
Characterization of the mating type (MAT) locus in the Phialocephala fortinii s.l. – Acephala applanata species complex
Pascal L. Zaffarano a, Angelo Duo a and Christoph R. Grunig a
a Institute of Integrative Biology (IBZ), Forest Pathology and Dendrology, ETH Zurich, 8092 Zurich, Switzerland
... 184 185 2.5. Annotation of the MAT locus 186 187 Positions of open reading frames, transcription
start and poly-A motifs in 188 sequences were predicted with FGENESH (http://linux1.softberry.com/
berry. 189 phtml?topic=fgenesh&group=programs&subgroup=gfind). ...
Eukaryotic Cell
2010 doi:10.1128/EC.00161-10
Co-localization of Amanitin and a Candidate Toxin-Processing Prolyl Oligopeptidase in Amanita Basidiocarps
Hong Luo, Heather E. Hallen-Adams, John S. Scott-Craig, and Jonathan D. Walton
Department of Energy Plant Research Laboratory, Michigan State University, E. Lansing MI 48824
... AbPOPA and AbPOPB, and two hybridizing clones were sequenced completely. 11 FGENESH
(www.softberry.com) was used to predict proteins ab initio using the 12 Coprinopsis cinerea model.
Each predicted protein was then used to search GenBank nr 13 using BLASTP. ...
BMC Plant Biology
2010, 10:145doi:10.1186/1471-2229-10-145
Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa
Hu et al.,
1 Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China
2 Current address: Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
... putative pseudogenes or incorrect annotations, and manual reannotation was performed to correct
and reannotate the putative NACs using online web server FGENESH (http://linux1.softberry.com/
berry.phtml) [59]. In this endeavor, seven sequences encoding only ...
Bioorganic & Medicinal Chemistry
Volume 18, Issue 12, 15 June 2010, Pages 4542-4546 doi:10.1016/j.bmc.2010.04.058
Identification of csypyrone B1 as the novel product of Aspergillus oryzae type III polyketide synthase CsyB
Yasuyo Seshime a, †, Praveen Rao Juvvadi b, ‡, Katsuhiko Kitamoto b, Yutaka Ebizuka c and Isao Fujii a
a School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
b Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
... These sequences were hand annotated by using FGENESH program (Softberry, Inc.) and/or
GeneID program. 25 Acknowledgements We thank Dr. D. Wakana for measurement of the
physicochemical properties of the compound, and Dr. T. Kushiro for helpful suggestions. ...
PNAS
January 5, 2010 vol. 107 no. 1 472-477 doi: 10.1073/pnas.0908007107
Angiosperm genome comparisons reveal early polyploidy in the monocot lineage
Tang, Haibao,Bowers, John E.,Wang, Xiyin,Paterson, Andrew H.
aPlant Genome Mapping Laboratory and
bDepartment of Plant Biology, University of Georgia, Athens, GA 30602
... set (Sbi1.4) from the Joint Genomics Institute (19), and the grapevine gene set from Genoscope
(3). Two Musa balbisiana BACs (AC226052.1 and AC226053.1) were downloaded from GenBank,
with putative gene models predicted using FGENESH (http://www.softberry.com). ...
BMC Plant Biology
2010, 10:25 6doi:10.1186/1471-2229-10-256
Functional divergence of the NIP III subgroup proteins involved altered selective constraints and positive selection
Qingpo Liu and Zhujun Zhu
College of Agriculture and Food Science, Zhejiang A & F University, Lin'an, Hangzhou 311300, China
... Programs InterProScan [45] and Page 14. ConPred II [46] were utilized to detect conserved
domains and predict the putative transmembrane regions (TMs), respectively. FgeneSH
(http://linux1.softberry.com/) was employed to predict the gene structures of candidates identified. ...
BMC Plant Biology
2010, 10:180 doi:10.1186/1471-2229-10-180
Structure and evolution of Apetala3, a sex-linked gene in Silene latifolia
Cegan et al.,
1 Laboratory of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i.Kralovopolska 135, CZ-612 65 Brno, Czech Republic
2 Department of Plant Biology, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
... software [48] (http://genes.mit.edu/GENSCAN.html) and FGENESH [49] (http://linux1.softberry.
com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind). ORFs were found with
ORF Finder [50] (http://www.ncbi.nlm.nih.gov/projects/gorf/) and a ...
BMC Plant Biology
2010, 10:135 doi:10.1186/1471-2229-10-135
Transcriptional regulation of the grape cytochrome P450 monooxygenase gene CYP736B expression in response to Xylella fastidiosa infection
Cheng et al.,
1 San Joaquin Valley Agricultural Science Center, USDA-ARS 9611 South Riverbend Avenue, Parlier, CA 93648, USA
2 Department of Biology, California State University, Fresno, CA 93740, USA
... a grape genomic database (GenBank Accessions: AM475392.1, CAAP02000243.
1, CAAP02005006.1) using the BLAST (http://www.ncbi.nlm.nih.gov/) and FGENESH
(http://www.softberry.com/berry.phtml) programs. A pair ...
BMC Genomics
2010, 11:179 doi:10.1186/1471-2164-11-179
Characterization of the ovine ribosomal protein SA gene and its pseudogenes
Broeke et al.,
1 Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium
2 Departamento de Mejora Genetica Animal, INIA, Ctra La Coruna Km 7.5, Madrid 28040, Spain
... Promoter sequences were searched with CISTER, Neural Network Promoter Prediction, FPROM and TFsearch [36,38-40].
... 36. FGENESH Webserver [http://linux1.softberry.com] ...
Functional Plant Biology
2010 37, 194–205.
Cloning and characterisation of ZmZLP1, a gene encoding an endoplasmic reticulum-localised zinc transporter in Zea mays
Xu Y, Wang B, Yu J, Ao G, Zhao Q
A State Key Laboratory of Agribiotechnology, China Agricultural University, Beijing 100193, China.
... The ZmZIP genomic sequences of Zea mays contigs were from http://maize.tigr.org/release5.
0/azm5.shtmL and were annotated for open reading frames using the gene prediction algorithms
of FGenesH (http://www.softberry.com); the others are in GenBank (http://www.ncbi.nlm ...
PLoS Biol
2010, vol. 8, num. 2, e1000313
Genome sequence of the pea aphid Acyrthosiphon pisum
Rozas Liras et al.,
... 2007-04628 award to ACCW. FgenesH models were donated by Softberry, Inc. This
research was additionally supported in part by the Intramural Research Program
of the NIH, National Library of Medicine. The funders had no ...
BMC Plant Biology
2010, 10:246
Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy
Gonzalez et al.,
Molecular Genetics Department, Center for Research in Agricultural
Genomics CRAG (CSIC-IRTA-UAB), Jordi Girona, 18-26, 08034 Barcelona, Spain
... setting the minimum identity parameter to 92. In some cases, the FGENESH annotation software
at http://linux1.softberry.com/berry.phtml, with Arabidopsis as plant model, was used to
complement or improve the Augustus annotation. The predicted coding ...
Plant Physiology
152:1772-1786 (2010)
Genomic Analysis of Wild Tomato Introgressions Determining Metabolism- and Yield-Associated Traits
Kamenetzky et al.,
Instituto de Biotecnologia, Instituto Nacional de Tecnologia Agropecuaria, and Consejo Nacional de Investigaciones Cientificas y Tecnicas, B1712WAA Castelar, Argentina (L.K., R.A., S.B., F.C.); Departamento de Botanica, Instituto de Biociencias, Universidade de Sao Paulo, Sao Paulo 05508–900, Brazil (F.d.G., L.B., M.-A.V.S., M.R.)
... S. pennellii BAC/cosmid full-length sequences as well as three S. lycopersicum BAC clones,
C04HBa0331L22, C07HBa0061J13, and C11HBa0062I24, were annotated using two different
gene prediction programs: FGENESH (www.softberry.com; Salamov and Solovyev, 2000 ...
PLoS Pathog
2010 6(4): e1000846. doi:10.1371/journal.ppat.1000846
SREB, a GATA Transcription Factor That Directs Disparate Fates in Blastomyces dermatitidis Including Morphogenesis
and Siderophore Biosynthesis
Gauthier et al.,
1 Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America, 2 Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
... blast.ncbi.nlm.nih.gov/Blast.cgi). FGENESH was used to identify predicted exons
and introns in the SREB gene (www.softberry.com). Generation of null mutants. Two
vectors, pBTS4-KO1 and pBTS4-KO2, were used to delete.
Mol Genet Genomics.
2010 Feb;283(2):135-45. Epub 2009 Dec 19
Genome-wide discovery of DNA polymorphism in Brassica rapa
Park S, Yu HJ, Mun JH, Lee SC.
Department of Horticultural Crop Research, National Institute of Horticultural and Herbal Science, RDA, Suwon, 441-440, Republic of Korea.
. 2009). A list of BAC clones with GenBank accession numbers is provided in Table
S1. Ab initio gene prediction for the BAC sequences was obtained by using the
FGENESH program (www.softberry.com) based on a B. rapa matrix. ...
Developmental & Comparative Immunology
Volume 34, Issue 4, April 2010, Pages 465-473 doi:10.1016/j.dci.2009.12.007
In search of the origin of FREPs: Characterization of Aplysia californica fibrinogen-related proteins
A.M. Gorbushin, Y.V. Panchin, and N.V. Iakovleva
Institute of Evolutionary Biochemistry and Physiology RAS, pr. Torez 44, Saint-Petersburg 194223, Russia
... contigs having even weak similarity to juxtaposed IgSF and FreD domains were retrieved from
the nucleotide database and the coding region was preliminary identified by several invertebrate
gene prediction models using FGeneSH software (http://linux1.softberry.com/berry ...
Microbiology
156 (2010), 278-286; DOI 10.1099/mic.0.033886-0
A tyrosine O-prenyltransferase catalyses the first pathway-specific step in the biosynthesis of sirodesmin PL
Anika Kremer and Shu-Ming Li
Philipps-Universitat Marburg, Institut fur Pharmazeutische Biologie, Deutschhausstrasse 17A, D-35037 Marburg, Germany
... Computer-assisted sequence analysis. FGENESH (SoftBerry; http://linux1.softberry.com/)
and the DNASIS software package (version 2.1; Hitachi Software Engineering) were used
for exon/intron prediction and sequence analysis, respectively. ...
Genome Biology and Evolution
2009 Vol. 1 265-277; doi:10.1093/gbe/evp025
Origin and Diversification of Land Plant CC-Type Glutaredoxins
M. Ziemann*, M. Bhave* and S. Zachgo**
*Environment and Biotechnology Centre, Faculty of Life and Social SciencesSwinburne University of Technology, Hawthorn, Victoria, Australia
**Department of Botany, University of Osnabruck, Osnabruck, Germany
... gene models. In cases of low conservation of exon sequences and lack of transcript
information, FGENESH hidden Markov model-based gene structure prediction
(http://linux1.softberry.com/berry.phtml) was utilized. Values ...
Current Genetics
Volume 55, Number 3 / June, 2009 pp. 253-262
The telomere-linked helicase (TLH) gene family in Magnaporthe oryzae: revised gene structure reveals a novel TLH-specific protein motif
Cathryn J. Rehmeyer, Weixi Li, Motoaki Kusaba and Mark L. Farman
(1) Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA
(2) Department of Biology, University of Kentucky, Lexington, KY 40546, USA
... Dean et al. 2005). The masked sequences were then used for gene prediction with
Fgenesh (Salamov and Solovyev 2000) trained on M. oryzae sequences (Softberry,
http://www.softberry.com). Various gene prediction tools ...
Nature
461, 1135-1138 (22 October 2009) | doi:10.1038/nature08498
A transposon-induced epigenetic change leads to sex determination in melon
Martin et al.,
(1) INRA-CNRS, UMR1165, Unite de Recherche en Genomique Vegetale, 2 rue Gaston Cremieux, F-91057 Evry, France
(2) Plateforme de Cytologie et d’Imagerie Vegetale, Institut Jean Pierre Bourgin, INRA, 78026 Versailles Cedex, France
... After assembly, two forms of gene annotation were performed: (1) ab initio gene prediction with
GENSCAN (http://genes.mit.edu/GENSCAN.html),
GeneMark.hmm (http://exon.gatech.edu/
GeneMark/eukhmm.cgi) and FGENESH (http://www.softberry.com/berry.phtml); and (2 ...
Journal of Equine Veterinary Science
2009 Volume 29, Issue 6, Pages 519-526
Search for Polymorphism in Exon 2 of the Equine Leptin Gene
N. Huff, D. Thompson Jr., K. Bondioli
... View Within Article. Splicing donor and acceptor consensus sequences were located at the
putative exon/intron borders. The predicted splice sites at the intron/exon boundaries were
analyzed using a computer program (FGeneSH, Softberry, Inc., Mount Kisco, NY). ...
Molecular Genetics and Genomics
Volume 282, Number 2 / August, 2009, pp. 205-215
Genome-wide analysis of conservation and divergence of microsatellites in rice
Manish Roorkiwal 1, Atul Grover 1 and Prakash C. Sharma 1
(1) University School of Biotechnology, Guru Gobind Singh Indraprastha University, Kashmere Gate, Delhi, 110403, India
.. 1.6.2 (Softberry; downloadable from http://www.molquest.com) prior to the alignment. This allowed
much higher number of queries to be handled per day compared to a maximum of 25 per day
when FGENESH was accessed through World Wide Web portal of Softberry. ...
Russian Journal of Plant Physiology
Volume 56, Number 4 / July, 2009, pp.532-539
Delimitation of the fgr gene for rice fragrance to a 28-kb DNA fragment
Ding et al.,
(1) College of Agriculture and Biotechnology, China Agricultural University, Beijing, 100094, China
(2) High-Tech Research Center, Shandong Academy of Agricultural Science, Jinan, Shandong, 250100, China
... region. The sequence analysis of this fragment using FGENESH (http:/www.softberry.
com) predicted three candidate genes encoding putative 3-methyllcrotonyl- CoA
carboxylase, putative isoleucyl-tRNA synthetase, and BADH2. ...
BMC Evolutionary Biology
2009, 9:271 doi:10.1186/1471-2148-9-271
The evolution of Brassica napus FLOWERING LOCUST paralogues in
the context of inverted chromosomal duplication blocks
Jing Wang et al.,
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China and 2Rothamsted
Research, Harpenden, Herts, AL5 2JQ, UK
... Sequence analysis The coding sequences and amino acids ofBnFT paralogues were predicted
using the software "Softberry FGENESH" online service (http://linux1.softberry.com/berry.phtml). ...
"Softberry NSITE-PL" online service (http://linux1.softberry.com/berry.phtml). ...
Theor Appl Genet.
2009 May;118(8):1509-17. Epub 2009 Mar 6.
Fine mapping SPP1, a QTL controlling the number of spikelets per panicle, to a BAC clone in rice (Oryza sativa)
Liu T, Mao D, Zhang S, Xu C, Xing Y.
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, 430070, Wuhan, China.
... Putative ORF prediction in 107 kb region The putative open reading frame (ORF) in the 107-kb
region was predicted by the online software FGENESH on the basis of the gene structure available
on the Internet (http://linux1.softberry.com/berry.phtml?topic=fgenesh& ...
Cited by 1 - Related articles - All 3 versions
PLoS One.
2009; 4(9): e6981 doi: 10.1371/journal.pone.0006981.
Identifying and Characterizing a Novel Protein Kinase STK35L1 and Deciphering Its Orthologs and Close-Homologs in Vertebrates
Pankaj Goyal, 1* Antje Behring, 1 Abhishek Kumar, 2 and Wolfgang Siess 1
1Institute for Prevention of Cardiovascular Diseases, University of Munich, Munich, Germany
2University of Bielefeld, Bielefeld, Germany
... This region was highly conserved among mammals (Figure 3B Figure 3 ). We
investigated this region for coding sequences manually and by using different gene
prediction software such as FGENESH (www.softberry.com). ...
Molecular Immunology
Volume 46, Issues 8-9, May 2009, Pages 1679-1687
The immunoglobulin heavy chain locus in the reptile Anolis carolinensis
Francisco Gambon Deza, Christian Sanchez Espinel and Susana Magadan Mompo
aUnidad de Inmunologia, Hospital do Meixoeiro, Carretera de Madrid s/n°, Vigo 36210, Pontevedra, Spain
bInstituto Superior de Saude do Alto Ave (ISAVE), Quinta de Matos, Geraz do Minho, 4830-31 PVL, Portugal
... The constant region genes and exons were obtained by comparison with those already described
for E. macularius. A dotplot was made with E. macularius and A. carolinensis sequences using
the DNASTAR (lasergene), FGENESH and FEX software (http://www.softberry.com). ...
The Plant Genome
doi: 10.3835/?plantgenome.2009.01.0001
vol. 2 no. 3 211-223
Retrotransposons within Syntenic Regions between Soybean and Medicago truncatula and Their Contribution to Local Genome Evolution
Bindu Joseph et al.,
Dep. of Agronomy, Iowa State Univ., Ames, IA 50011
... (2006). BAC Sequence Analysis. The LG I UBP12 region BAC sequences were annotated using
gene prediction programs FGENESH (www.softberry.com) and GeneMark (Lomsadze et al., 2005,
http://opal.biology.gatech.edu/GeneMark/eukhmm.cgi; verified 30 July 2009). ...
Plant Science
Volume 176, Issue 3, March 2009, Pages 352-359
Characterization of six novel NAC genes and their responses to abiotic stresses in Gossypium hirsutum L.
Chaomin Meng, Caiping Cai, Tianzhen Zhang and Wangzhen Guo
National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, PR China
... Additionally, assembled sequences were compared to exon predictions from FGENESH
(http://www.softberry.com). From these gene predictions, gene-specific primers (Table
1) were designed for PCR from cDNA and genomic DNA. ...
J Biosci.
2009 Jun;34(2):251-61.
Physical mapping, expression analysis and polymorphism survey of resistance gene analogues on chromosome 11 of rice.
Ghazi IA, Srivastava PS, Dalal V, Gaikwad K, Singh AK, Sharma TR, Singh NK, Mohapatra T.
National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110 012, India.
... The FASTA form of each BAC/PAC clone sequence was downloaded as a text file one
by one. Gene prediction was performed for each clone using FGENESH (www.
softberry.com) trained for monocot species (Salamov and Solovyer 2000). ...
TAG Theoretical and Applied Genetics
Volume 118, Number 6 / April 2009 pp. 1027-1034
Identification and mapping of Pi41 , a major gene conferring resistance to rice blast in the Oryza sativa subsp. indica reference cultivar, 93-11
Qinzhong Yang 1, 2, Fei Lin 1, Ling Wang 1 and Qinghua Pan 1
Laboratory of Plant Resistance and Genetics, College of Resources and Environmental Sciences, South China Agricultural University, 510642 Guangzhou, China
... markers. Flanking markers were used to identify candidate NBS- LRR genes, with
the help of GENSCAN (http://genes.mit. edu), FGENSH (http://sun1.softberry.com)
and RiceGAAS (http://rgp.dna.affrc.go.jp) software. The sequence ...
Developmental & Comparative Immunology
Volume 33, Issue 4, April 2009, Pages 547-558
Identification of an Atlantic salmon IFN multigene cluster encoding three IFN subtypes with very different expression properties
Baojian Sun, Borre Robertsen, Zhiqiang Wang and Bin Liu
aDepartment of Marine Biotechnology, Norwegian College of Fishery Science, University of Tromso, N-9037 Tromso, Norway
bInstitute of Oceanology, Chinese Academy of Sciences, Qingdao and Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
... 2.2. Bioinformatics. Annotation of genes in genomic sequences was performed by
analysis with the programs Genscan (http://genes.mit.edu/GENSCAN.html) and
Fgenesh (http://softberry.com) combined with manual inspections. ...
The Plant Genome
doi: 10.3835/?plantgenome2008.09.0007
vol. 2 no. 1 93-101
Gene Content and Distribution in the Nuclear Genome of Fragaria vesca
Pontaroli et al.,
Dep. of Genetics, Univ. of Georgia, Athens, GA 30602;
... Gordon et al., 1998). Fosmid Sequence Annotation. Ab initio gene prediction was
performed on each fosmid sequence using FGENESH (Softberry, Inc., Mount Kisco,
NY) with the Arabidopsis training set. All the obtained predicted ...
Planta
Volume 229, Number 4 / March, 2009, pp. 885-897
Regulation of the cellulose synthase-like gene family by light in the maize mesocotyl
Harrie van Erp 1, 2 and Jonathan D. Walton 1
(1) Department of Energy-Plant Research Laboratory, Michigan State University, E. Lansing, MI 48824, USA
(2) Present address: Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
... Supplementary Table S1). Proteins encoded by the MAGI sequences were
determined using the FGENESH monocotyledon ab initio gene prediction program
(http://www.softberry.com) (Yao et al. 2005). The predicted protein ...
BMC Plant Biol.
2009 Jul 17;9:93.
Identification of three wheat globulin genes by screening a Triticum aestivum BAC genomic library with cDNA from a diabetes-associated globulin.
Loit E, Melnyk CW, MacFarlane AJ, Scott FW, Altosaar I.
Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada.
... sequence of Glo-3A were analyzed to identify a potential promoter using TSSP, a plant promoter
recognition program (www.softberry.com) and PlantProm database [24]. A ... (http://www.ncbi.nih.
gov/gorf/gorf.html) and FGENESH 3.0 alpha (www.softberry.com) ...
Plant Molecular Biology
Volume 70, Numbers 1-2 / May, 2009, pp. 47-61
Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat
Naxin Huo et al.,
(1) Genomics and Gene Discovery Research Unit, USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
(2) Department of Plant Sciences, University of California, Davis, CA 95616, USA
... In addition, coding regions in the BAC sequences were also predicted using FGENESH (http://
www.softberry.com) set for a monocot model. Predicted genes were then compared to the
nonredundant and dbEST databases of NCBI (March 2008) using BLASTN and BLASTX. ...
Molecular Plant
2009 doi:10.1093/mp/ssp064
The CELLULOSE-SYNTHASE LIKE C (CSLC) Family of Barley Includes Members that Are Integral Membrane Proteins Targeted to the Plasma Membrane
Dwivany et al.,
Plant Cell Biology Research Centre, School of Botany, University of Melbourne Victoria 3010, Australia
... the 5' and 3' directions. Most of the intron/exon boundaries predicted by FGENESH
(www.softberry.com) in the HvCSLC1 and HvCSLC4 genomic sequences were
confirmed from EST data. A schematic representation of the ...
Plant Physiology and Biochemistry
Volume 47, Issue 7, July 2009, Pages 650-652
Evidence of a sirtuin gene family in grapevine (Vitis vinifera L.)
Matteo Busconi, Serena Reggi, Corrado Fogher and Luigi Bavaresco
aIstituto di Botanica e Genetica vegetale, Universita Cattolica del Sacro Cuore, Via Emilia Parmense, 84 29100 Piacenza, Italy
bIstituto di Frutti-Viticoltura, Universita Cattolica del Sacro Cuore, Via Emilia Parmense, 84 29100 Piacenza, Italy
... When appropriate, the prediction of hypothetical gene structure was performed using
the following software in parallel: FGENESH (http://linux1.softberry.com), GeneMark
(http://exon.gatech.edu), and GENSCAN (http://genes.mit.edu). ...
Fungal Genetics and Biology
Volume 46, Issue 9, September 2009, Pages 695-706
Mutations to LmIFRD affect cell wall integrity, development and pathogenicity of the ascomycete Leptosphaeria maculans
Angela P. Van de Wouw, Filomena A. Pettolino, Barbara J. Howlett and Candace E. Elliott
aSchool of Botany, The University of Melbourne, Vic. 3010, Australia
... study are listed in Table 1. The coding region of a gene flanking the T-DNA insertion (subsequently
referred to as LmIFRD) and a gene downstream of the T-DNA (subsequently referred to as
LmcABH-like) were predicted using FGENESH software (http://www.softberry.com/berry ...
BMC Evol Biol.
2009 Jul 19;9:168.
Evolution of a subtilisin-like protease gene family in the grass endophytic fungus Epichloe festucae
Bryant MK, Schardl CL, Hesse U, Scott B.
Institute of Molecular Biosciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
... reading frames for SLP and unlinked non-SLP genes were identified using FGENESH, an
HMM-based gene structural prediction using the Fusarium graminearum parameters
(http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfi nd). ...
Functional & Integrative Genomics
Volume 9, Number 1 / February, 2009, pp. 97-108
The 172-kb genomic DNA region of the O. rufipogon yld1.1 locus: comparative sequence analysis with O. sativa ssp. japonica and O. sativa ssp. indica
Beng-Kah Song et al.,
(1) School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
(2) Genome Dynamics Program, Scottish Crop Research Institute, Dundee, DD2 5DA, UK
... affrc.go.jp/usr-bin/login.cgi) and was aided by the rice training set of the gene-finding program
GeneMark.hmm (Lukashin and Borodovsky 1998, http://genemark.biology. gatech.edu/GeneMark/),
fgenesh (http://www.softberry. com/berry.phtml) and RiceHMM (Sakata et al. ...
Genetics
Published Articles Ahead of Print: October 12, 2009,
doi:10.1534/genetics.109.106922
Fine Mapping and Haplotype Structure Analysis of a Major Flowering Time Quantitative Trait Locus on Maize Chromosome 10
Ducrocq et al.,
INRA
... c0111K09) were analyzed using TE-Nest (KRONMILLER and WISE 2008) and RepeatMasker
(http://www.repeatmasker.org/) in order to localize transposable elements. Masked sequences
were annotated using Fgenesh (http://linux1.softberry.com/berry.phtml, version 2.6). ...
Plant Molecular Biology Reporter
Volume 27, Number 4 / December, 2009, pp. 526-533
The Promoters of Forisome Genes MtSEO2 and MtSEO3 Direct Gene Expression to Immature Sieve Elements in Medicago truncatula and Nicotiana tabacum
Noll et al.,
1) Institut fur Biochemie und Biotechnologie der Pflanzen der Westfalischen Wilhelms, Universitat Munster, Hindenburgplatz 55, Munster, 48143, Germany
(2) Department of Biology, University of York, Heslington, York, YO10 5DD, UK
... The MtSEO promoter sequences were aligned using the Lasergene software package v7.1
(DNAstar, Madison, WI, USA). Putative TATA box sequences were identified by analyzing the
corresponding genomic clone using the FGENESH program (http://www.softberry.com). ...
Molecular Genetics and Genomics
Volume 281, Number 5 / May, 2009, pp. 565-578
Characterization of cyclophilin-encoding genes in Phytophthora
Pamela Hui Peng Gan 1 , Weixing Shan 1, 2, Leila M. Blackman 1 and Adrienne R. Hardham 1
1) Plant Cell Biology Group, Research School of Biological Sciences, School of Biology, The Australian National University, GPO Box 475, Canberra, ACT, 2601, Australia
(2) Present address: College of Plant Protection, Northwest A & F University, Yangling, China
... eng/scripts/01_13.html. Genes were predicted from genomic sequences using
FGENESH (Softberry Inc., Mount Kisco, NY, USA), with diatom-speciWc parameters
and GENSCAN (Chesnick et al. 2000). To analyze pro- moter ...
Heredity.
2009 Mar;102(3):266-73. Epub 2008 Nov 12
Evolutionary fate of rhizome-specific genes in a non-rhizomatous Sorghum genotype
Jang et al.,
Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
... GAP2 (Huang, 1994) programs. Alternatively, gene structures were predicted by
FGE- NESH gene prediction software (http://sun1.softberry. com/berry.phtml) with
the training set for monocot plants. Orthologs of Oryza sativa ...
Molecular Breeding
Volume 24, Number 4 / November, 2009, pp. 433-446
Development of SNP markers linked to the L locus in Capsicum spp. by a comparative genetic analysis
Hee-Bum Yang 1, Wing Yee Liu 1, Won-Hee Kang 1, Molly Jahn 2 and Byoung-Cheorl Kang
(1) Department of Plant Science, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul, 151-921, Korea
(2) College of Agriculture and Life Science, University of Wisconsin, Madison, WI 53706, USA
... National University, Korea). BAC sequence annotation The FGENESH program
(http://linux1.softberry.com/ berry.phtml) was used to predict genes from the contig
sequence based on tomato organism informa- tion. To search for ...
BMC Biol.
2009 Jul 23;7:43.
Features of the ancestral bilaterian inferred from Platynereis dumerilii ParaHox genes
Hui et al.,
Department of Zoology, University of Oxford, Oxford, UK
... To find additional genes in these contigs besides the ParaHox genes, the entire contig sequences
were scanned with GENSCAN and FGENESH (implemented at www.softberry.com [79]), and
all predicted peptide sequences searched against Genbank with BLASTP. ...
Genetics
Vol. 181, 405-419, February 2009, doi:10.1534/genetics.108.093583
Molecular Analysis of a Large Subtelomeric Nucleotide-Binding-Site–Leucine-Rich-Repeat Family in Two Representative Genotypes of the Major Gene Pools of Phaseolus vulgaris
Geffroy et al.,
* Institut de Biotechnologie des Plantes, UMR-CNRS 8618, INRA, Universite Paris-Sud, 91 405 Orsay, France, Department of Chromosome Biology, University of Vienna, 1030 Vienna, Austria
... Ann Arbor, MI). The genomic sequence was annotated by using the gene prediction
program Fgenesh (Softberry website) and was manually edited by a homology search
against available databases. The genomic sequence ...
Molecular Biology and Evolution
2009 26(7):1651-1661; doi:10.1093/molbev/msp076
Sixty Million Years in Evolution of Soft Grain Trait in Grasses: Emergence of the Softness Locus in the Common Ancestor of Pooideae and Ehrhartoideae, after their Divergence from Panicoideae
Charles et al.,
* Unite de Recherches en Genomique Vegetale (UMR INRA 1165–CNRS 8114UEVE), Organization and evolution of Plant Genomes, Evry, France
Plant Genome Mapping Laboratory, University of Georgia
... We used the gene prediction given by the program FGENESH (http://www.softberry.com; with
the Monocot matrix) as well as BlastN and BlastX and TBlastX alignments against dbEST
(http://www.ncbi.nlm.nih.gov/), SwissProt (http://expasy.org/sprot/), and synteny with ...
BMC Genomics.
2009 Aug 13;10:376.
Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response
O'Rourke et al.,
Department of Genetics, Developmental and Cellular Biology, Iowa State University, Ames, Iowa 50011, USA.
... QTL (Figure 1, Additional files 1 and 2). Sequences of the delineated iron QTL
regions were analyzed using FGENESH (www.softberry.com) using Arabidopsis
as the training model to identify gene structure predictions. The ...
Fungal Genetics and Biology
Volume 46, Issue 5, May 2009, Pages 353-364
Biosynthesis of the cyclooligomer depsipeptide bassianolide, an insecticidal virulence factor of Beauveria bassiana
Yuquan Xu et al.,
aSW Center for Natural Products Research and Commercialization, Office of Arid Lands Studies, College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706-6800, USA
bDepartment of Entomology, College of Agriculture and Life Sciences, The University of Arizona, 1140 E. South Campus Dr., Tucson, AZ 85721-0036, USA
... closure. Sequence assembly was done with Sequencher 4.7 (Gene Codes Corp).
HMM-based gene models were built with FGENESH (Softberry) using the F.
graminearum and the Aspergillus nidulans training sets. The models ...
Theor Appl Genet.
2009 Apr;118(6):1199-209. Epub 2009 Feb 15.
ps-2, the gene responsible for functional sterility in tomato, due to non-dehiscent anthers, is the result of a mutation in a novel polygalacturonase gene
Gorguet B, Schipper D, van Lammeren A, Visser RG, van Heusden AW.
Graduate School of Experimental Plant Sciences, Wageningen UR Plant Breeding, PO Box 386, 6700 AJ, Wageningen, The Netherlands
... genetic map. ORF4, a putative polygalacturonase gene, mapped the clos- est to
the ps-2 locus (Fig. 2). Subsequently, the putative introns and exons were identiWed
using the FGENSH soft- ware of Softberry. The candidate ...
Molecular & Cellular Proteomics
October 1, 2009, 8, 2368-2381.
In Planta Proteomics and Proteogenomics of the Biotrophic Barley Fungal Pathogen Blumeria graminis f. sp. hordei
Bindschedler et al.,
School of Biological Sciences, The University of Reading, P. O. Box 221, Reading RG6 6AS, United Kingdom,
Centre for Bioinformatics, Imperial College, Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom
... to predict ORFs. Putative ORFs were determined with the FGENESH prediction program
using either the Leptosphaeria maculans or the Sclerotinia sclerotiorum ORF prediction
models (SoftBerry, Inc.). Putative classical secretion ...
PLoS Pathog.
2009 January; 5(1): e1000261.
Genomic Survey of the Non-Cultivatable Opportunistic Human Pathogen, Enterocytozoon bieneusi
Akiyoshi et al.,
1Division of Infectious Diseases, Department of Biomedical Sciences, Tufts Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of America
2Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
... ECU08_1090/ECU08_1100). Introns. DNA sequences of contigs greater than 10 kb
were analyzed by FGENESH (http://www.softberry.com; [44]), an HMM-based gene
structure prediction program, to identify putative introns. For the ...
Cited by 11 - Related articles - All 7 versions
BMC Res Notes.
2009; 2: 206.
Intragenic tandem repeats in Daphnia magna: structure, function and distribution
Isabelle Colson,1 Louis Du Pasquier,1 and Dieter Ebert 1
1Basel University, Zoological Institute, Vesalgasse 1, CH-4051 Basel, Switzerland
... 18. Salamov A, Solovyev V:Ab initio gene finding in Drosophila genomic DNA. Genome
Res 2000,10: 516-522. 19. Fgenesh [http://linux1.softberry.com/berry.phtml?topic=
fgenesh&group=programs&sy bgroup=gfind]. Page 13. - 12 - 20. ...
World Journal of Microbiology and Biotechnology
Volume 25, Number 6 / June, 2009, pp. 989-995
Characteristic analysis of transformants in T-DNA mutation library of Monascus ruber
Shao et al.,
(1) College of Food Science and Technology, Huazhong Agricultural University, Hongshan District, 430070 Wuhan, Hubei, People’s Republic of China
... et al. 2004) was carried out to extend the DNA sequences flanking TAIL-PCR
products. Up to now, we have amplified eight full DNA sequences, which were
submitted to FGENESH (http://linux1.softberry.com/berry. phtml) to ...
PLoS Pathogens
January 2009, Volume 5, Issue 1, e1000261. doi:10.1371/journal.ppat.1000261
Genomic Survey of the Non-Cultivatable Opportunistic
Human Pathogen, Enterocytozoon bieneusi
Akiyoshi et al.,
1 Division of Infectious Diseases, Department of Biomedical Sciences, Tufts Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of
America, 2 Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
... ECU08_1090/ECU08_1100). Introns. DNA sequences of contigs greater than 10 kb
were analyzed by FGENESH (http://www.softberry.com; [44]), an HMM-based gene
structure prediction program, to identify putative introns. For the ...
PNAS
February 17, 2009 vol. 106 no. 7 2295-2300 doi: 10.1073/pnas.0807350106
Duplicate genes increase expression diversity in closely related species and allopolyploids
Misook Ha a,b,c, Eun-Deok Kim a and Z. Jeffrey Chen a,b,c,d
Sections of aMolecular Cell and Developmental Biology and
dIntegrative Biology
bCenter for Computational Biology and Bioinformatics, and
cInstitute for Cellular and Molecular BiologyOne University StationA-4800University of TexasAustinTX 78712
... The sequencing reads were assembled and edited. A. arenosa genes were annotated using
FGENESH (www.softberry.com) and BLAST against cDNA sequences of A. thaliana. Annotated
genomic sequences are deposited in GenBank (accession no. FJ461780). ...
Plant Physiology
149:286-296 (2009)
A Germin-Like Protein Gene Family Functions as a Complex Quantitative Trait Locus Conferring Broad-Spectrum Disease Resistance in Rice
Manosalva et al.,
Bioagricultural Sciences and Pest Management and Program in Plant Molecular Biology, Colorado State University, Fort Collins, Colorado 80523–1177 (P.M.M., R.M.D, J.E.L.); Plant Pathology, Kansas State University, Manhattan, Kansas 66502–5502 (P.M.M.);
... cgi) using the HTGS database. FGENESH (http://www.softberry.com/berry.phtml) was
used to predict putative oxalate oxidase and OsGLP from significant rice bacterial
artificial chromosome hits. All nucleotide and inferred amino ...
Plant Journal.
60(1):181-193, October 2009.
Genome organization of the tomato sun locus and characterization of the unusual retrotransposon Rider
Jiang N, Gao D, Xiao H, van der Knaap E.
Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.
... Tomato eIF4a6 was used to assess equal loading and mRNA and cDNA quality. Primer sequences
are listed in Table S3. Annotations TOP. The gene sequences were identified using the ab initio
gene prediction program FGENESH (http://www.softberry.com/berry.phtml ). ...
Nucleic Acids Research
2009, Vol. 37, Database issue D750-D754 doi:10.1093/nar/gkn887
SpBase: the sea urchin genome database and web site
R. Andrew Cameron, Manoj Samanta, Autumn Yuan, Dong He and Eric Davidson
Center for Computational Regulatory Genomics, Beckman Institute 139–74, California Institute of Technology, Pasadena, CA 91104, USA
... were independently employed by individual groups to arrive at sets of gene models
for eventual annotation: Gnomon at NCBI (13); FgenesH from Softberry (14,15 ...
Nature
2008, 4doi:10.1038/nature07410
The Phaeodactylum genome reveals the evolutionary history of diatom genomes.
Bowler et al.
1. CNRS UMR8186, Department of Biology, Ecole Normale Supe'rieure, 46 rue d'Ulm, 75005 Paris, France
2. Stazione Zoologica 'Anton Dohrn', Villa Comunale, I-80121 Naples, Italy
... Gene predictors used for these annotations included ab initio Fgenesh 12 trained on sets of known
genes and reliable homology-based gene models from P. tricornutum and T.pseudonana, and homology-based Fgenesh+ 12
and Genewise 13 seeded by BLASTX alignments against sequences in the NCBI non-redundant protein set. ...
Nature
2008, 452, 949 - 955.
The genome of the model beetle and pest Tribolium castaneum.
Richards et al.
1. Human Genome Sequencing Cente
2. Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
... Work at the BCM-HGSC was funded by grants from the NHGRI and USDA. FgenesH and FgenesH++ analysis
was donated by Softberry Inc. This research was additionally supported in part by the Intramural...
Nature
2008, 452, 991 - 996.
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
Ming et al.
Hawaii Agriculture Research Center, Aiea, Hawaii 96701, USA
Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
61801, USA
...in training ab initio gene prediction software Augustus, GlimmerHMM and SNAP. Ab initio gene prediction software Fgenesh, Genscan and
TWINSCAN were trained on Arabidopsis. Spliced alignments of proteins from the plant division of...
Nature
Volume 453 Number 7198 pp1064 - 1071 (19 Jun 2008), doi: 10.1038/nature06967
The amphioxus genome and the evolution of the chordate karyotype.
Putnam et al.
# Department of Energy Joint Genome Institute, Walnut Creek California 94598, USA
# Center for Integrative Genomics, Department of Molecular and Cell Biology, University of
California, Berkeley, California 94720, USA
... A\Supplementary Note 3. Annotation of protein coding genes
3.1 Expressed sequence tag sequencing.
cDNA libraries for amphioxus were prepared from gastrula and neurula
stage embryos, and from
larvae as described by 6, and a single library was created for
Petromyzon marinus (sea lamprey).
Approximately 32,000 expressed sequence tags (ESTs) were attempted
from each library.
(Supplementary Table S6).
3.2 Gene prediction, functional annotation and quality control.
The JGI Annotation Pipeline was used for annotation of the amphioxus
v1.0 assembly described
here. The pipeline includes the following steps: (1) repeat masking,
(2) mapping ESTs, full length
cDNAs, and putative full length known genes, (3) gene structure
prediction using several methods,
(4) protein functional annotation using several methods, and (5)
combining gene predictions into a
non redundant representative set of gene models, which are subject to
genome-scale analysis. The
genomic sequence, predicted genes and annotations of amphioxus,
together with available
evidence, are available at the JGI Genome Portal
(www.jgi.doe.gov/Amphioxus) and from GenBank
under accession number ABEP01000000.
Transposons were masked using RepeatMasker 7 tools and a custom
library of manually curated
repeats (see above Supplementary Note 2.4). 480,070 ESTs were
clustered into 77,402 consensus
sequences and both individual ESTs and consensus sequences were mapped
onto genome assembly
using BLAT4.
Gene predictors used for annotation of amphioxus v1.0 included ab
initio FGENESH 8, homology-
based FGENESH+ 8, homology-based GENEWISE 9, and EST-based ESTEXT (Grigoriev,
unpublished, available upon request). ...
Nature
452, 88 - 92 (06 Mar 2008), doi: 10.1038/nature06556, Letter
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
Martin et al.,
MR 1136, INRA-Nancy Universite, Interactions Arbres/Microorganismes, INRA-Nancy, 54280
Champenoux, France.
...in the scaffold assembly (Supplementary Table 2). Genome annotation Gene models were predicted
using FgenesH, homology-based FgenesH+ (ref. 18) and Genewise, as well as EuGAne and TwinScan, and alignments of several complementary DNA...
Nature
451, 193 - 196 (10 Jan 2008), doi: 10.1038/nature06453, Letter
Identification of the sex genes in an early diverged fungus
Alexander Idnurm, Felicia J. Walton, Anna Floyd, Joseph Heitman
Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North
Carolina 27710, USA.
...were searched with BLASTp, BLASTn or tBLASTn programs.
Gene predictions from unannotated genomic DNA were made with FGENESH
software using the settings for Schizosaccharomyces pombe. HMG domains
were aligned in ClustalW, in MacClade...
Genetics
Published Articles Ahead of Print: December 15, 2008,
doi:10.1534/genetics.108.093583
Molecular Analysis of a Large Subtelomeric NBS-LRR Family in Two Representative Genotypes of the Major Gene Pools of Phaseolus vulgaris
Valerie et al.,
Institut de Biotechnologie des Plantes
University of Vienna
Institut Pasteur
... Arbor, MI, USA). The genomic sequence was annotated by using the gene prediction
program Fgenesh (Softberry website) and was manually ...
PLoS Genet.
2008 November; 4(11): e1000261.
Zebrafish Mutants calamity and catastrophe Define Critical Pathways of Gene–Nutrient Interactions in Developmental Copper Metabolism
Erik C. Madsen and Jonathan D. Gitlin
Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
... This contig was scanned for potential genes using the FGENESH program (www.softberry.
com) and comparing to the Ensembl database (www.ensembl.org). ...
BMC Plant Biology
2008, 8:133 doi:10.1186/1471-2229-8-133
The lipoxygenase gene family: a genomic fossil of shared polyploidy between
Glycine max and Medicago truncatula
Shin et al.,
Department of Plant Science, Seoul National University, Seoul 151-921, Korea
... FgeneSH on an Arabidopsis matrix, because the resultswere better suited for BLASTZ
resultsthan that of the Medicago matrix (http://www.softberry.com). Each ...
BMC Genomics
2008, 9:555 doi:10.1186/1471-2164-9-555
New insights into the origin of the B genome of hexaploid wheat: Evolutionary
relationships at the SPA genomic region with the S genome of the diploid
relative Aegilops speltoides
Salse et al.,
Organisation and Evolution of Plant Genomes (OEPG), UMR INRA 1165 - CNRS 8114
UEVE - Unite de Recherche en Genomique Vegetale (URGV). 2, rue Gaston Cremieux,
CP5708, 91057 Evry cedex. France.
Gene structures and putative functions were identified by combining results of
BLASTN and BLASTX alignments against dbEST (http://www.ncbi.nlm.nih.gov/) and
SwissProt databases (http://expasy.org/sprot/), with results of 2 gene predictor programs,
Page 17
15
Eugene [53] with rice (Oryza sativa) training version and FgeneSH [54] (with default
parameters (http://sun1.softberry.com/).
BMC Genetics
2008, 9:78 doi:10.1186/1471-2156-9-78
Genomic Complexity of the Variable Region-Containing Chitin-Binding Proteins
in Amphioxus
Dishaw et al.,
All Children’s Hospital,Department of Molecular Genetics,801SixthStreet South,St. Petersburg,FL
33701,USA
... html),FGENESH and FGENESH+ (http://linux1.softberry.com/all.htm) or
genomescan[63,66] (http://genes.mit.edu/genomescan. html).Details ...
BMC Evolutionary Biology
2008, 8:115
doi:10.1186/1471-2148-8-115
Roots of angiosperm formins: the evolutionary history of plant FH2
domain-containing proteins
Michal Grunt, Viktor Zarsky and Fatima Cvrckova
Department of Plant Physiology, Faculty of Sciences, Charles University, Vinicna' 5,
CZ 128 43 Praha 2, Czech Republic
... For each new gene, splice sites were predicted using at least three of the following
eukaryotic gene-prediction programs: GeneMark.hmm [84], FGENESH [85] at the
Softberry, Inc. website [86] ...
Appl. Environ. Microbiol.
December 2008 doi:10.1128/AEM.01889-08
Telomere organization in the ligninolytic basidiomycete Pleurotus ostreatus
Gumer Perez, Jasmyn Pangilinan, Antonio G. Pisabarro, and Lucia Ramirez
Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006 Pamplona, Spain; DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
... The Hidden 153 Markov Model (HMM)-based program FGENESH was used for web-based
gene 154 prediction (http://www.softberry.com/berry.phtml). ...
International Journal of Integrative Biology
2008 v.3 No 1, 50
SNP in Granule Bound Starch Synthase-I (GBSS-I) gene in Indian rice genotypes
SK Srivastava, U Roy
... The genes for both the BACs have been predicted using FGENESH software
(http://www.softberry.com), which revealed the presence of 23 and 34 genes respectively ...
International Journal of Plant Genomics
Volume 2008, Article ID 391259, 8 pages doi:10.1155/2008/391259
Conserved Microsynteny of NPR1 with Genes Encoding
a Signal Calmodulin-Binding Protein and a CK1-Class Protein
Kinase in Beta vulgaris and Two Other Eudicots
David Kuykendall, Jonathan Shao, and Tammy Murphy
Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture,
10300 Baltimore Avenue, Building 004, Room 120, Beltsville, MD 20705, USA
... The sequence contig was
screened for coding sequence using a combination of the
following programs: GeneMark [18, 19] for eukaryotes
(http://exon.gatech.edu/GeneMark/eukhmm.cgi), GenScan
(http://genes.mit.edu/GENSCAN.html), FGENESH (http://
softberry.com/), and GRAIL ...
BMC Genomics
2008, 9:563 doi:10.1186/1471-2164-9-563
The UDP-glucosyltransferase multigene family in Bombyx mori
Huang et al.,
The Key Sericultural Laboratory of Agricultural Ministry, Institute of Sericulture and
Systems Biology, Southwest University, Chongqing 400715, China
... query sequence and its flanking regions were extracted, and put into Softberry
database for predicting new genes by using FGENESH taking the available insect...
CURRENT SCIENCE
VOL. 95, NO. 8, 25 OCTOBER 2008
Identification of candidate gene-based
markers (SNPs and SSRs) in the zinc and iron
transporter sequences of maize (Zea mays L.)
Arti Sharma and R. S. Chauhan
Advanced Centre of Hill Bioresources and Biotechnology, CSK HP Agricultural University, Palampur 176 062, India
Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, P.O. Dumehar Bani,
Kandaghat, Solan 173 215, India
... for open reading frames (ORFs), including the promoter regions and the 3?UTRs using
gene prediction algorithms of FGenesH (http:// sun1.softberry.com/berry ...
Yeast
Sequencing Report 2008 Volume 25 Issue 9, Pages 673 - 679
The gap-filling sequence on the left arm of chromosome 2 in fission yeast Schizosaccharomyces pombe
Sasaki et al.,
ASPEX Division, Research Centre, Asahi Glass Co., Ltd., Japan
... Corporation). ORFs, introns and exons were predicted using FGENESH
(http://www.softberry.com/) (Sala- mov et al., 2000) on an Sz. ...
Insect Biochemistry and Molecular Biology
Volume 38, Issue 12, December 2008, Pages 1111-1120
A genomewide survey of homeobox genes and identification of novel structure of the Hox cluster in the silkworm, Bombyx mori
Chai et al.,
The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China
... The intergenic sequences where the lost homeobox genes were found were further put
into the Softberry database for predicting new genes by using the FGENESH ...
International Journal of Integrative Biology
2008 Volume 2 N.3 pp.153-156
Sprome: A database on promoters of abiotic stress inducible genes in rice
R Sundheep, L Arul, P Nagarajan, P Balasubramanian
...FGENESH, a gene prediction tool based on Hidden Markov Model (HMM) was used to predict the presence of plausible
Exon/UTR in the putative promoter region (http://www.softberry.com/berry ...
Trends in Biochemical Sciences
Volume 33, Issue 12, December 2008, Pages 577-582
Eukaryote polyphosphate kinases: is the 'Kornberg' complex ubiquitous?
Paul Hooley, Michael P. Whitehead and Michael R.W. Brown
School of Applied Sciences, Wulfruna Street, University of Wolverhampton, Wolverhampton, WV1 1SB, UK
... Genome projects perform automatic annotations using gene-finding programs such as
FGENESH (Softberry) or Artemis (Sanger Centre), with somewhat arbitrary cut ...
Heredity
12 Nov 2008, doi: 10.1038/hdy.2008.119
Evolutionary fate of rhizome-specific genes in a non-rhizomatous Sorghum genotype
C S Jang, T L Kamps, H Tang, J E Bowers, C Lemke, A H Paterson
1. 1Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
2. 2Plant Genomics Lab, Department of Applied Plant Sciences Technology, Kangwon National University, Chuncheon, Korea
... Alternatively, gene structures were predicted by FGENESH gene prediction software (http://sun1.softberry.com/berry.phtml) with the training set for monocot plants. Orthologs of Oryza sativa corresponding to...
Theor Appl Genet
DOI 10.1007/s00122-008-0888-y
Fine genetic mapping of xa24, a recessive gene for resistance
against Xanthomonas oryzae pv. oryzae in rice
Xiaoming Wu, Xianghua Li, Caiguo Xu and
Shiping Wang
National Key Laboratory of Crop Genetic Improvement,
National Center of Plant Gene Research (Wuhan),
Huazhong Agricultural University, Wuhan 430070, China
... Gene prediction analysis was performed with the programs GENSCAN (http://genes.mit.
edu/GENSCAN.html), FGE- NESH (http://www.softberry.com/berry.phtml) and Gene ...
Gene
Volume 424, Issues 1-2, 15 November 2008, Pages 71-79 doi:10.1016/j.gene.2008.07.027
SRWD: A novel WD40 protein subfamily regulated by salt stress in rice (Oryzasativa L.)
Ji Huang et al.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
... Using corresponding genomic sequence, the opening read frame (ORF) was predicted
by Fgenesh program at Softberry server (http://www.softberry.com) and this ...
Molecular Plant
2008 1(5):830-838; doi:10.1093/mp/ssn045
Fine Mapping of Spr3, a Locus for Spreading Panicle from African Cultivated Rice (Oryza glaberrima Steud.)
Ji-Jing Luo, Wei Hao, Jian Jin, Ji-Ping Gao and Hong-Xuan Lin
National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
... The counterpart DNA sequences of the interval defined by the markers L4359 and L4264
of Nipponbare were predicted with FGENESH of Softberry (www.softberry.com ...
Genome
Volume 51, Number 6, 1 June 2008 , pp. 452-464(13)
Comparative genomic analysis of the whale (Pseudorca crassidens) PRNP locus
Kim, Dae-Won et al.
... Ab initio gene pre- diction was performed on the genomic sequences using FGENESH
(SoftBerry, Inc., Mount Kisco, New York; http:// www.softberry.ru/berry.phtml ...
Fungal Genetics and Biology
Volume 45, Issue 11, November 2008, Pages 1487-1496 doi:10.1016/j.fgb.2008.08.009
Characterization of the atromentin biosynthesis genes and enzymes in the homobasidiomycete Tapinella panuoides
Patrick Schneider, Sarah Bouhired and Dirk Hoffmeister
Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universitat, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany
... The Aspergillus or Phanerochaete search algorithms of FGENESH (Softberry, Mount
Kisco, NY) were used to predict gene structures and exon/intron junctions. 2.5. ...
Molecular Phylogenetics and Evolution
Volume 49, Issue 1, October 2008, Pages 349-355 doi:10.1016/j.ympev.2008.04.025
Molecular evolution and diversification of plant cysteine proteinase inhibitors: New insights after the poplar genome
M. Margis-Pinheiro et al.
a Programa de Pos-graduacao em Genetica e Biologia Molecular, Departamento de Genetica, Universidade Federal do Rio Grande do Sul, Brazil
b Programa de Pos-graduacao em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Brazil
c Departamento de Bioquimica, Instituto de Ciencias Basicas da Saude, Universidade Federal do Rio Grande do Sul, Brazil
... Genomic sequences from Arabidopsis thaliana and Oryza sativa were also analyzed
in the FGENESH gene structure prediction program (http://www.softberry.com/). ...
J. Biol. Chem.
Vol. 283, Issue 40, 26859-26868, October 3, 2008 doi:10.1074/jbc.M804979200
Ergot Alkaloid Biosynthesis in Aspergillus fumigatus:
OVERPRODUCTION AND BIOCHEMICAL CHARACTERIZATION OF A 4-DIMETHYLALLYLTRYPTOPHAN N-METHYLTRANSFERASE
Ole Rigbers and Shu-Ming Li
From the Heinrich-Heine-Universitat Dusseldorf, Institut fur Pharmazeutische Biologie und Biotechnologie, Universitatsstrasse 1, D-40225 Dusseldorf, Germany and the Philipps-Universitat Marburg, Institut fur Pharmazeutische Biologie, Deutschhausstrasse 17A, D-35037 Marburg, Germany
... Computer-assisted Sequence Analysis-FGENESH (Softberry, Inc.) and the DNASIS software
package (version 2.1; Hitachi Software Engineering, San Bruno, CA) were ...
Gene
Volume 418, Issues 1-2, 15 July 2008, Pages 41-48 doi:10.1016/j.gene.2008.04.005
Is crab duplex-specific nuclease a member of the Serratia family of non-specific nucleases?
V. E. Anisimova et al.
a Shemiakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117871 Moscow, Russia
b Evrogen JSC, Miklukho-Maklaya 16/10, 117871 Moscow, Russia
... The putative N- and/or C-terminal terminal ends were searched in the genomic
regions using FGENESH software (http://sun1.softberry.com). ...
Int J Plant Genomics
2008: 348621. Published online 2008 June 18. doi: 10.1155/2008/348621.
Development in Rice Genome Research Based on Accurate Genome Sequence
Takashi Matsumoto, Jianzhong Wu, Baltazar A. Antonio, and Takuji Sasaki
Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, 2-1-2, Kannondai, Tsukuba, Ibaraki 3058602, Japan
... It retrieves rice sequences from GenBank and analyzes them with gene prediction
programs such as Genscan [31] and FgeneSH (http://www.softberry.com/berry.phtml ...
Molecular Genetics and Genomics
Volume 279, Number 5 / May 2008 pp. 473-480
Construction of a fosmid library of cucumber ( Cucumis sativus ) and comparative analyses of the eIF4E and eIF(iso)4E regions from cucumber and melon ( Cucumis melo )
J. D. F. Meyer, W. Deleu3, J. Garcia-Mas and M. J. Havey
(1) Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
(2) Vegetable Crops Unit, Agricultural Research Service, US Department of Agriculture, Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
(3) IRTA, Centre de Recerca en Agrigenomica CSIC-IRTA-UAB, Carretera de Cabrils Km 2, 08348 Cabrils (Barcelona), Spain
... 1997; http://www.ncbi.nlm.nih.gov/ BLAST/), GENESCAN (Burge and Karlin 1997; http://
www.genes.mit.edu/GENSCAN.html), and FGENESH (http://www.softberry.com). ...
Molecular Breeding
Volume 22, Number 4 / November 2008 pp. 593-602
Cloning and sequence diversity analysis of GmHs1 pro-1 in Chinese domesticated and wild soybeans
Cuiping Yuan et al.
(1) Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/Crop Germplasm & Biotechnology, Ministry of Agriculture, Beijing, 100081, China
(2) Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Taiyuan, 030031, China
... ORF and amino acid sequence were predicted with FGENESH 2.5 software (http://www.
softberry.com) and used as a basis to estimate sequence diversity at ...
Genetics.
Published Articles Ahead of Print: September 9, 2008, doi:10.1534/genetics.108.092304
Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat
Mathieu Charles et al.
1 URGV (INRA-CNRS-UEVE),
2 CEA Genoscope,
3 Murdoch University,
4 INRA
... Six genes (of known or unknown function) and two putative genes were identified using
the FGENESH prediction software (http://www.softberry.
com) and by identification of homologs in rice (Figure ...
Gene
Volume 420, Issue 2, 1 September 2008, Pages 135-144 doi:10.1016/j.gene.2008.05.019
Expression analysis of rice A20/AN1-type zinc finger genes and characterization of ZFP177 that contributes to temperature stress tolerance
Ji Huang et al.
State key laboratory of crop genetics and germplasm enhancement, Nanjing Agricultural University, Nanjing 210095, China
... By database searching and FgeneSH prediction (http://www.softberry.com), it was
found 12 putative proteins containing both A20 and AN1 zinc finger motifs in ...
Molecular Breeding
Volume 22, Number 4 / November 2008 pp. 603-612
Gene identification and allele-specific marker development for two allelic low phytic acid mutations in rice ( Oryza sativa L.)
Zhao et al.
(1) IAEA-Zhejiang University Collaborating Center, National Key Laboratory of Rice Biology and Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
(2) Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
(3) Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, 1400 Vienna, Austria
... et al. 2004). Gene prediction was made using the FGENESH program available
on http://www.softberry.com/berry.phtml. PCR primers ...
Crop Sci
48:S-49-S-68 (2008)
Structural Features of the Endogenous CHS Silencing and Target Loci in the Soybean Genome
Jigyasa H. Tuteja and Lila O. Vodkin
Dep. of Crop Sciences, 384 ERML, 1201 W. Gregory Dr., Univ. of Illinois, Urbana, IL 61801.
... For ab initio predictions, FGeneSH with the Medicago truncatula-based training
set (http://www.softberry.com; verified 9 Jan. 2008) was run. ...
Gene
Volume 411, Issues 1-2, 31 March 2008, Pages 27-37
Multiple tandem gene duplications in a neutral lipase gene cluster in Drosophila
Irene Horne and Victoria S. Haritos
CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601, Australia
... Genomic regions containing significant sequence similarity in multiple regions were
then examined for genes using FGENESH on Softberry (http://www.softberry.com ...
J. Virol.
July 2008, p. 6697-6710, Vol. 82, No. 13 doi:10.1128/JVI.00212-08
A single Banana streak virus integration event in the banana genome as the origin of infectious endogenous pararetrovirus (EPRV)
Philippe Gayral et al.,
CIRAD BIOS, UMR Biologie et Ge'ne'tique des Interactions Plante-Parasite (BGPI), TA 4-54/K Campus international de Baillarguet, F-34398 Montpellier Cedex 5, France;
... genes (FgenesH for monocot plants (44), softberry software (http://www.softberry.
com) and 184 ACCEPTED at Google Indexer on May 20, 2008 jvi.asm.org ...
Int. J. Mol. Sci.
2008, 9, 1717-1729; DOI: 10.3390/ijms9091717
Are the Genes nadA and norB Involved in Formation of
Aflatoxin G1
Kenneth C. Ehrlich, Leslie L. Scharfenstein Jr., Beverly G. Montalbano and
Perng-Kuang Chang
Southern Regional Research Center, 1100 Robert E. Lee Blvd, P.O. Box 19687, New Orleans, LA
70179, USA
... a coding sequence with a single intron are predicted for nadA in A. parasiticus
SU-1 and BN008 isolates based on an analysis using the Softberry FGENESH coding ...
New Phytologist
Volume 179 Issue 1 Page 196-208, July 2008
Magnaporthe grisea avirulence gene ACE1 belongs to an infection-specific gene cluster involved in secondary metabolism
Jerome Collemare et al.,
UMR5240 CNRS/UCB/INSA/BAYER CropScience, 14-20 Rue Pierre Baizet, 69263 Lyon cedex 09, France
... FgenesH (http://www.softberry.com) was used to identify introns using
Schizosaccharomyces pombe and Neurospora crassa matrices. ...
Chembiochem
Volume 9 Issue 7, Pages 1019 - 1023, 2008
Synthetic Strategy of Nonreducing Iterative Polyketide Synthases and the Origin of the "Classical Starter-Unit Effect"
Jason M. Crawford, Dr., Anna L. Vagstad, Karen P. Whitworth, Kenneth C. Ehrlich, Dr., Craig A. Townsend, Dr.
1Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA, Fax: (+1) 410-516-8420
2Southern Regional Research Center, United States Department of Agriculture, 1100 RE Lee Boulevard, New Orleans, LA 70124, USA
... by using the revised sequence re- sulted in an alternative splicing pattern that
translated through the GXCXG motif (FGENESH, http://www.softberry.com, Sup ...
Trends in Plant Science
doi:10.1016/j.tplants.2008.02.009
Diamonds in the rough: mRNA-like non-coding RNAs
Linda A. Rymarquis, James P. Kastenmayer, Alexander G. Huttenhofer and Pamela J. Green
Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
213501 Hamlet Square Court, Germantown, MD 20874, USA
3Innsbruck Biocentre, Division of Genomics and RNomics, Innsbruck Medical University, Fritz-Pregl Stra?e 3, 6020 Innsbruck, Austria
... The remaining RNAs are screened for ORFs, using programs such as GeneMark [25],
GenScan [26], Fgenesh (www.softberry.com) or EST scan [27]. ...
Mycological Research
Volume 112, Issue 2, February 2008, Pages 216-224
Processing sites involved in intron splicing of Armillaria natural product genes
Mathias Misieka and Dirk Hoffmeister
Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universitat, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany
... For exon/intron identification we used the Aspergillus and Phanerochaete mode
implemented in FGENESH (Softberry, Mount Kisco, NY) and Augustus (Stanke & ...
Current Bioinformatics
Volume 3, Number 2, May 2008 , pp. 87-97(11)
Genome Annotation in Plants and Fungi: EuGene as a Model Platform
Foissac, Sylvain et al.,
... Simultaneously, a specific version of FGenesH was built for M. truncatula
by the SoftBerry company (http://www.- softberry.com/). ...
Mol Biol Evol.
25(5):892-902; doi:10.1093/molbev/msn029
Comparative analysis of the MIR319a microRNA locus in Arabidopsis and related Brassicaceae
Norman Warthmann, Sandip Das, Christa Lanz and Detlef Weigel
Department of Molecular Biology, Genome Center, Max Planck Institute for Developmental Biology, D-72076 Tubingen, Germany
... 2005) and FGENESH (www.softberry.com) were used to predict putative novel ORFs,
and validated using TBLASTN against the NCBI nr database. 6 Page 7. ...
FEMS Yeast Research
Volume 8 Issue 3 Page 432-441, May 2008
The endogenous adrenodoxin reductase-like flavoprotein arh1 supports heterologous cytochrome P450-dependent substrate conversions in Schizosaccharomyces pombe
Kerstin M. Ewen, Burkhard Schiffler, Heike Uhlmann-Schiffler, Rita Bernhardt, Frank Hannemann
Department of Biochemistry, Saarland University, Saarbrucken, Germany; and Department of Medical Biochemistry, Saarland University, Homburg, Germany
... The program fgenesh (http://www.softberry.com) was applied to identify the position
and composition of the arh1 gene as well as to deduce the amino acid ...
Eukaryotic Cell
February 2008, p. 368-378, Vol. 7, No. 2
A Botrytis cinerea Emopamil Binding Domain Protein, Required for Full Virulence, Belongs to a Eukaryotic Superfamily Which Has Expanded in Euascomycetes
A. Gioti et al.,
UMR1290 BIOGER-CPP, INRA, Route de St-Cyr, 78026 Versailles, France
... were improved manually for seven genes, one of which was not predicted by automatic
software Blastx alignment data; FGenesh (http://www.softberry.com) and ...
DNA Research
2008 15(2):93-102; doi:10.1093/dnares/dsn001
Sequence Level Analysis of Recently Duplicated Regions in Soybean [Glycine max (L.) Merr.] Genome
Kyujung Van et al.,
Department of Plant Science, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, South Korea
... Also, gene annotation was conducted with the web-based gene prediction programs
FGENESH (http://sun1.softberry.com/berry.phtml) and GeneMark (http://exon.gatech ...
Insect Biochemistry and Molecular Biology
Volume 38, Issue 3, March 2008, Pages 331-345
Annotation and expression profiling of apoptosis-related genes in the yellow fever mosquito, Aedes aegypti
Bart Bryanta, Carol D. Blairb, Ken E. Olsonb and Rollie J. Clem
Molecular, Cellular, and Developmental Biology Program, Arthropod Genomics Center, Division of Biology, Ackert Hall, Kansas State University, Manhattan, KS, USA
bArthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
... Genscan (http://genes.mit.edu/GENSCAN.html) and fgenesh (http://www.SoftBerry.com)
were used to predict genes and complete missing regions of some EST contigs. ...
Plant Physiology
146:940-951 (2008)
Characterization of the Monoterpene Synthase Gene tps26, the Ortholog of a Gene Induced by Insect Herbivory in Maize
Changfa Lin et al.,
Waksman Institute, Rutgers University, Piscataway, New Jersey 08855 (C.L., B.S., Z.X., H.K.D.); Department of Plant Biology, Rutgers University, New Brunswick, New Jersey 08901 (B.S., Z.X., H.K.D.);
... Analysis of the sequence by the gene-finding program Fgenesh (www.softberry.com)
predicted that, like stc1, tps26 consisted of seven exons. ...
Disease Markers
Volume 24, Number 2 / 2008 Pages 111-117
Analysis of Crohn's disease-related CARD15 polymorphisms in Spanish patients with idiopathic uveitis
N. Rodriguez-Perez, A. Aguinaga-Barrilero, Marina B. Gorrono-Echebarria, Mercedes Perez-Blas, J.M. Marti'n-Villa
Inmunologia, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
Servicio de Oftalmologia, Hospital Universitario Principe de Asturias, Alcala de Henares, Madrid, Spain
... Analysis carried out with GEN- SCAN (http://genes.mit.edu/GENSCAN.html), FCGENESH
(http://www.softberry.com/berry.phtml) and GRAIL (http://grail.lsd.ornl.gov ...
Crop Sci
48:S-49-S-68 (2008)
Structural Features of the Endogenous CHS Silencing and Target Loci in the Soybean Genome
Jigyasa H. Tuteja and Lila O. Vodkin
Dep. of Crop Sciences, 384 ERML, 1201 W. Gregory Dr., Univ. of Illinois, Urbana, IL 61801.
... For ab initio predictions, FGeneSH with the Medicago truncatula-based training
set (http://www.softberry.com; verified 9 Jan. 2008) was run. ...
Journal of Integrative Plant Biology
Volume 50 Issue 4 Page 466-474, April 2008
Cell-wall Invertases from Rice are Differentially Expressed in Caryopsis during the Grain Filling Stage
Yong-Qin Wang et al.,
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China; Graduate School of the Chinese Academy of Sciences, Beijing 100049, China
... Splice site prediction was carried out with programs GENSCAN (http://genes.mit.edu/
GENSCAN.html) and FGENESH (http://www.softberry.com/berry.phtml). ...
Journal of Integrative Plant Biology
Volume 50 Issue 1 Page 62-75, January 2008
Cloning and Expression Analysis of Rice Sucrose Transporter Genes OsSUT2M and OsSUT5Z
Ai-Jun Sun et al.,
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China; 2Graduate School of the Chinese Academy of Sciences, Beijing 100049, China
... The ORF of these two potential sucrose transporters were figured out by FGENESH
(http://www.softberry.com/), and primers used for RT-PCRs were designed by ...
Molecular Plant
2008 1(3):471-481; doi:10.1093/mp/ssn014
Mutation of a Gene in the Fungus Leptosphaeria maculans Allows Increased Frequency of Penetration of Stomatal Apertures of Arabidopsis thaliana
Candace E. Elliott, Harjono, and Barbara J. Howlett
School of Botany, The University of Melbourne, Melbourne, Vic 3010, Australia
Current address: Laboratory of Forest Protection, Faculty of Forestry, Gadjah Mada University, Yogyakarta, Indonesia 55281
... using a primer walking strategy. Genes on the cosmid were predicted using
FGENESH software (www.softberry.com). A BLASTp search (www ...
Plant Physiology
146:200-212 (2008)
Recurrent Deletions of Puroindoline Genes at the Grain Hardness Locus in Four Independent Lineages of Polyploid Wheat
Wanlong Li, Li Huang and Bikram S. Gill
Wheat Genetic and Genomic Resources Center, Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506–5502
... Protein-coding genes were predicted using the program FGENESH (http://sun1.softberry.
com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind) with the ...
Genomics
Volume 91, Issue 5, May 2008, Pages 467-475
Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets
Nicolas Buisinea 1, Hadi Quesneville, 2 and Vincent Colot
Unite' de Recherche en Ge'nomique Ve'ge'tale, INRA UMR1165–CNRS UMR8114–Universite' d'Evry Val d'Essonne, 2 rue Gaston Cre'mieux, 91057 Evry, France
Laboratoire Bioinformatique et Ge'nomique, Institut Jacques Monod, Tour 42, 2 place Jussieu, 75251 Paris, France
... The functional content of each RU sequence was predicted using FGENESH
(http://sun1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind ...
Nucleic Acids Research,
2008, Vol. 36, Database issue D298-D302
ChromDB: The Chromatin Database
Karla Gendler, Tara Paulsen and Carolyn Napoli
BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA
... In many cases, we have derived our own transcript models from genomic sequences
using FGNESH or FGENESH+ licensed from Softberry (http://www.softberry.com). ...
Nature Biotechnology
26, 553 - 560 (2008)
Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)
Diego Martinez et al.,
Los Alamos National Laboratory/Joint Genome Institute, PO Box 1663, Los Alamos, New Mexico 87545, USA.
Novozymes, Inc., 1445 Drew Ave., Davis, California 95618, USA.
... an ab initio gene predictor, Fgenesh 37 , specifically trained for this genome,
and two homology-based gene predictors, Fgenesh+ (http://www.softberry.com) and ...
Genome Res.
17:1389-1398, 2007
Conrad: Gene prediction using conditional random fields
David DeCaprio et al.,
The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
... data. Conrad was trained on the entire reference set and Fgenesh was trained
by Softberry (Salamov and Solovyev 2000 Go). Results. ...
PNAS
July 10, 2007 | vol. 104 | no. 28 | 11844-11849
A GeneTrek analysis of the maize genome
Renyi Liu et al.,
Department of Genetics, University of Georgia, Athens, GA 30602; and Department of Agronomy, Iowa State University, Ames, IA 5001
... BAC sequences were first subject to ab initio gene prediction with FGENESH
(www.softberry.com) using the matrix for monocot plants. ...
Antonie van Leeuwenhoek
Volume 91, Number 4 / May, 2007 pp. 373-391
Tagging target genes of the MAT1-2-1 transcription factor in Fusarium verticillioides ( Gibberella fujikuroi MP-A)
Anita Keszthelyi et al.,
Agricultural Biotechnology Center, Szent-Gyorgyi A. u. 4, H-2100 Godollo, Hungary
.. Sequence data were analyzed with the Lasergene (DNAStar Inc., Madison, Wisconsin,
USA) software package and the FGENESH program (www.softberry.com). ...
Genome
Volume 50, Number 6, 1 June 2007 , pp. 595-609(15)
Diversity of the trifunctional histidine biosynthesis gene (his) in cereal Phaeosphaeria species
Wang, Chih-Li et al.,
... acc. No. DQ312266) using the FGENESH program (http://www.softberry.com)
with As- pergillus as the organism parameter (Fig. 1). The ...
Current Genetics
Volume 52, Number 1 / July, 2007 pp. 11-22
Mating-type loci of heterothallic Diaporthe spp.: homologous genes are present in opposite mating-types
Satoko Kanematsu. Yoshihiko Adachi and Tsutae Ito
Apple Research Station, National Institute of Fruit Tree Science, NARO, Shimokuriyagawa, Morioka 020-0123, Japan
, National Agricultural Research Center for Tohoku Region, NARO, Akahira, Morioka 020-0198, Japan
... Genes, introns, exons and transcription initiation sites of Diaporthe W- and G-types
were predicted by analysis with FGENESH (http://www.softberry.com) on N ...
Plant Molecular Biology
Volume 65, Numbers 1-2 / September, 2007 pp. 189-203
Rapid evolution and complex structural organization in genomic regions harboring multiple prolamin genes in the polyploid wheat genome
Shuangcheng Gao et al.,
Key Laboratory of Crop Germplasm & Biotechnology, MOA, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, No. 12 South Street, Zhongguancun, Beijing, 100081, P.R. China
... FGENESH (http://www.softberry.com/ nucleo.html) and GENESCAN (http://genemark.
mit.edu/ GENESCAN.htm) were used for gene prediction. ...
Plant Molecular Biology
Volume 65, Number 4 / November, 2007 pp. 439-451
Molecular cloning and expression analysis of a monosaccharide transporter gene OsMST4 from rice ( Oryza sativa L.)
Yongqin Wang et al.,
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Beijing, 100101, China
... Splice site prediction was per- formed with programs GENSCAN (http://www.genes.mit.
edu/GENSCAN.html) and FGENESH (http://www. softberry.com/berry.phtml). ...
Plant Physiology
145:29-40 (2007)
Chlorophyll-Deficient Rice Mutant with Impaired Chlorophyllide Esterification in Chlorophyll Biosynthesis
Ziming Wu et al.,
National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China (Z.W., B.H., L.J., C.W., J.W.);
... 2, B and C). Within this region, two open reading frames (ORFs) were predicted
using the program FGENESH 2.2 (www.softberry.com). ...
TAG Theoretical and Applied Genetics
Volume 115, Number 2 / July, 2007 pp. 159-168
Physical mapping and identification of a candidate for the leaf rust resistance gene Lr1 of wheat
Ji-Wen Qiu et al.,
State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China
... tauschii lines were translated into protein sequences using the online gene prediction
program Fgenesh (http://sunl.Softberry.com/cgi-bin/programs/gWnd/ Fgenesh ...
Fungal Genetics and Biology
Volume 44, Issue 10, October 2007, Pages 1002-1010
Comparison of loline alkaloid gene clusters across fungal endophytes: Predicting the co-regulatory sequence motifs and the evolutionary history
Brandi L. Kutil et al.,
Department of Plant Pathology and Microbiology, Texas A&M University (2132), College Station, TX 77843-2132, USA
.. of coding sequences based on previously identified cDNAs ([Spiering et al., 2002]
and [Spiering et al., 2005]) and FGENESH (http://www.softberry.com/berry.phtml ...
Peptides
Volume 28, Issue 6, June 2007, Pages 1282-1291
Neuropeptide precursors in Tribolium castaneum
Andinet Amare and Jonathan V. Sweedler
Department of Chemistry and The Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
... The FGENESH version 2.5 (www.softberry.com) and Augustus version 1.8.2
(http://augustus.gobics.de/submission) gene prediction programs were used to predict ...
Mol. BioSyst.,
2007, 3, 794 - 802, DOI: 10.1039/b705803a
Distinctive expression and functional regulation of the maize (Zea mays L.) TOR kinase ortholog
Lourdes Teresa Agredano-Moreno, Homero Reyes de la Cruz, Leon Patricio
Martinez-Castilla and Estela Sanchez de Jimenez
... OsTOR was obtained with the Gene Builder system (http://www.itba.mi.cnr.it/webgene)
and confirmed with the FGENESH 2.4 program from the Softberry webpage (http ...
Plant Physiology and Biochemistry
Volume 45, Issue 1, January 2007, Pages 6-14
Computational identification and phylogenetic analysis of the MAPK gene family in Oryza sativa
Qingpo Liu and Qingzhong Xue
Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, No 268, Kaixuan Road, Hangzhou, Zhejiang 310029, China
... Redundant hits were removed by manual inspection. Gene structure prediction was
performed using the online web server FGENESH (http://www.softberry.com). 2.2. ...
Fungal Genetics and Biology
Volume 44, Issue 5, May 2007, Pages 415-429
Mating-type genes and the genetic structure of a world-wide collection of the tomato pathogen Cladosporium fulvum
Ioannis Stergiopoulos et al.,
Laboratory of Phytopathology, Wageningen University and Research Centre, Binnenhaven 5, 6709 PD Wageningen, The Netherlands
... Barcelona, Spain) and the FEX (Solovyev et al., 1994) and FGENESH (Salamov and Solovyev,
2000) programs from the MOLQUEST software package (Softberry Inc. ...
Nucleic Acids Research
(2007), doi:10.1093/nar/gkm768
ChromDB: The Chromatin Database
Karla Gendler, Tara Paulsen and Carolyn Napoli
BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA
... In many cases, we have derived our own transcript models from genomic sequences
using FGNESH or FGENESH+ licensed from Softberry (http://www.softberry.com). ...
Microbiology
153 (2007), 3409-3416;
A 7-dimethylallyltryptophan synthase from Aspergillus fumigatus: overproduction, purification and biochemical characterization
Anika Kremer, Lucia Westrich and Shu-Ming Li
Heinrich-Heine-Universitat Dusseldorf, Institut fur
Pharmazeutische Biologie und Biotechnologie, Universitatsstrasse 1, D-40225 Dusseldorf, Germany,
Eberhard-Karls-Universitat Tubingen, Pharmazeutische Biologie, Auf der Morgenstelle 8, D-72076
Tubingen, Germany
... FGENESH (Softberry; www.softberry.com/berry.phtml) and the DNASIS software package
(version 2.1; Hitachi Software Engineering) were used for intron prediction ...
General and Comparative Endocrinology
Volume 153, Issues 1-3, August-September 2007, Pages 59-63
Evolutionary conservation of bursicon in the animal kingdom
Tom Van Loy et al.,
Animal Physiology and Neurobiology, Laboratory for Developmental Physiology, Genomics and Proteomics, Zoological Institute, K.U.Leuven, Naamsestraat 59, B-3000, Belgium
... ncbi.nih.gov/gorf) and, in addition, were conducted to the gene prediction program
FGENESH based on hidden markov models, available on http://www.softberry.com ...
Fungal Genetics and Biology
Volume 44, Issue 2, February 2007, Pages 77-87
Extracellular oxidative systems of the lignin-degrading Basidiomycete Phanerochaete chrysosporium
Phil Kersten and Dan Cullen
Forest Products Laboratory, USDA, One Gifford Pinchot Drive, Madison, WI 53705, USA
... Predictions were based on ab initio methods Fgenesh (Salamov and Solovyev, 2000),
homology-based methods, Fgenesh+ (www.softberry.com) and Genewise (Birney and ...
Molecular Plant Pathology
Volume 8 Issue 1 Page 111-120, January 2007
Isolation and characterization of the mating type
locus of Mycosphaerella fijiensis, the causal agent of
black leaf streak disease of banana
LAURA CONDE-FERRAEZ et al.,
Centro de Investigacion Cientifica de Yucatan (CICY), Calle 43 no. 130, Chuburna
de Hidalgo, C.P. 97200, Merida, Yucatan, Mexico
... Identification of open reading frames (ORFs) and gene predictions were performed
using FGENESH and FGENESH+ software (SoftberryTM, http:/ / www.softberry.com ...
Chinese Science Bulletin
Volume 52, Number 7 / April, 2007 pp. 903-911
Genetic and physical mapping of AvrPi7 , a novel avirulence
gene of Magnaporthe oryzae using physical position-ready markers
Feng ShuJie, Wang Ling, Ma JunHong, Lin Fei and Pan QingHua
Laboratory of Plant Resistance and Genetics, College of Natural Resources and Environmental Science, South China Agricultural University, Guangzhou, 510642, China
Laboratory of Plant Protection, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
... for fine mapping of the Avr gene locus based on the se- quence of the candidate
genes predicted using the gene annotation system Softberry FGENESH (http://www. ...
Plant Molecular Biology
Volume 64, Number 5 / July, 2007 589-600
New insights into Oryza genome evolution: high gene colinearity
and differential retrotransposon amplification
Shibo Zhang et al.,
(1) Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
... BLASTN, BLASTX, and TBLASTX against TIGR’s Rice Gene Indices database and NCBI’s
nonredundant and dbEST databases; FGENESH (http:// www.softberry.com/nucleo ...
DNA AND CELL BIOLOGY
Volume 26, Number 6, 2007 Pp. 369-385
Genomics, Evolution, and Expression of TBPL2,
a Member of the TBP Family
CINZIA DI PIETRO et al.,
Dipartimento di Scienze Biomediche-Unita` di Biologia Genetica e BioInformatica, Universita` di Catania, Catania, Italy, EU.
Genomic sequences
were analyzed using several gene prediction tools
(GPTs): Genescan (http://genes.mit.edu/GENSCAN.html),
GeneMark (http://opal.biology.gatech.edu/GeneMark/index
.html), FGENESH (http://www.softberry.com/berry.phtml?topic
=gfind&prg=FGENESH),
Chinese Science Bulletin
Volume 52, Number 7 / April, 2007 912-921
Rapid genome evolution in Pms1 region of rice revealed by comparative sequence analysis
Yu JinSheng et al.,
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
... For gene prediction, the sequences were ana- lyzed with several gene prediction
programs including FGENESH (monocot training set, http://www.softberry. ...
Journal of Integrative Plant Biology
Volume 49 Issue 5 Page 655-663, May 2007
The 6-phosphogluconate Dehydrogenase Genes Are Responsive to Abiotic Stresses in Rice
Fu-Yun Hou, Ji Huang, Shan-Lin Yu and Hong-Sheng Zhang
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
... One assembled cDNA sequence containing a complete ORF (opening reading frame) of
1 524 bp was obtained using the FGENESH program (http://www.softberry.com) and ...
Molecular Plant Pathology
Volume 8 Issue 3 Page 307-319, May 2007
Molecular and cytological responses of Medicago truncatula
to Erysiphe pisi
DAWN FOSTER-HARTNETT et al.,
Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, St Paul, MN 55108, USA
... BAC sequences with > 98% identity were collected, corresponding coding regions were
predicted using FGENESH software (http://www.softberry.com), and the 1.5-kb ...
Plant Science
Volume 172, Issue 4, April 2007, Pages 708-721
Genome-wide analysis and identification of genes related to
potassium transporter families in rice (Oryza sativa L.)
R. Naga Amruthaa, P. Nataraj Sekhara, Rajeev K. Varshneyb and P.B. Kavi Kishora,
aDepartment of Genetics, Osmania University, Hyderabad 500007, India
bInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502325, India
... and Karlin, 1997; http:// genes.mit.edu/GENSCAN.html), GenomeScan [30];
http://genes.mit.edu/ genomescan.html), FGENESH [31]; http://www.softberry.com/berry ...
Molecular Biology and Evolution, 2007, doi:10.1093/molbev/msm116
PIF-like Transposons Are Common in Drosophila and Have Been Repeatedly Domesticated to Generate New Host Genes
Claudio Casola, A. Michelle Lawing, Esther Betran and Cedric Feschotte
Department of Biology University of Texas, Arlington
... The structure of each DPLG coding sequence was initially predicted using FGENESH
(http://www.softberry.com/berry.phtml) and refined by multialignment with ...
Journal of Virology,
June 2007, p. 6491-6501, Vol. 81, No. 12
Genomic and Morphological Features of a Banchine
Polydnavirus: Comparison with Bracoviruses and Ichnoviruses
Renee Lapointe et al.,
Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du PEPS, Quebec, Quebec G1V 4C7, Canada
... html), the Gene Construction Kit 2 program (Texco Inc.), Genchek v. 2061 (Ocimum
Biosolutions), and FGENESH, with the Apis mellifera settings (www.softberry.com ...
The Plant Journal
Volume 49 Issue 2 Page 173-183, January 2007
Characterization of the centromere and peri-centromere retrotransposons
in Brassica rapa and their distribution in related Brassica species
Ki-Byung Lim et al.,
1School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 702-701, Korea,
2Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea,
... Gene annotation was achieved using the web-based gene prediction program FGENE-SH
Arabidopsis ( http:/ / www.softberry.com/ berry.phtml ). Sequence analysis. ...
Journal of Molecular Evolution
Volume 64, Number 3 / March, 2007 354-363
Molecular Phylogeny, Evolution, and Functional Divergence of the
LSD1-Like Gene Family: Inference from the Rice Genome
Qingpo Liu 1 and Qingzhong Xue 1
(1) Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, P. R. China
... The FGENESH software (http://www.softberry.com) was used to predict the
intron/exon structure of putative rice LSD1-like genes. ...
BMC Microbiology
2007, 7:61 doi:10.1186/1471-2180-7-61
Structure and evolution of a proviral locus of
Glyptapanteles indiensis bracovirus
Christopher A Desjardins et al.,
The Institute for Genomic Research, a division of J. Craig Venter Institute, Rockville, Maryland, USA
...A combination of Softberry's FGENESH trained on the honey bee (Apis mellifera) and the Beijing Genome Institute's BGF trained on the silkmoth (Bombyx mori) were most accurate ...
...Gene models were generated with a variety of software: Softberry's FGENESH [77] using both the honey bee (Apis mellifera) and fruit fly (Drosophila melanogaster) training sets,...
PNAS
| May 1, 2007 | vol. 104 | no. 18 | 7705-7710
The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation
Brian Palenik et al.,
aScripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0202; cJoint Genome Institute and Stanford Human Genome Center, Stanford University School of Medicine, 975 California Avenue, Palo Alto, CA 94304;
... Gene prediction methods used for annotation of two Ostreococcus genomes included
ab initio Fgenesh (40), homology-based Fgenesh+ (SoftBerry), Genewise (41 ...
Nature Biotechnology
25, 319 - 326 (2007)
Published online: 4 March 2007 | doi:10.1038/nbt1290
Genome sequence of the lignocellulose-bioconverting and
xylose-fermenting yeast Pichia stipitis
Thomas W Jeffries et al.,
US Department of Agriculture, Forest Service, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, Wisconsin 53705, USA.
Department of Bacteriology, University of Wisconsin-Madison, 420 Henry Mall, Madison, Wisconsin 53706, USA.
... Gene prediction methods used for analysis of the P. stipitis genome include ab initio
Fgenesh 44 , homology-based Fgenesh+ (http://www.softberry.com/) and ...
Functional & Integrative Genomics
Volume 7, Number 1 / January, 2007 17-35
Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes
Nagendra K. Singh et al.,
Rice Genome Laboratory, National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
... Gene prediction was performed on individual BAC/PAC clones using FGENESH trained
for monocot species (http://www.softberry.com) (Salamov and Solovyev 2000). ...
Molecular Microbiology
Volume 64 Issue 3 Page 755-770, May 2007
Molecular analysis of the cercosporin biosynthetic gene
cluster in Cercospora nicotianae
Huiqin Chen, Miin-Huey Lee, Margret E. Daub, Kuang-Ren Chung
Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS), University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA.
... positions were deduced from comparisons of genomic and cDNA sequences and/or predicted
using the fgenesh gene-finding software at http://www.softberry.com. ...
Plant Physiology
144:623-636 (2007)
Molecular Evolution of Lysin Motif-Type Receptor-Like Kinases in Plants
Xue-Cheng Zhang et al.,
Division of Plant Sciences and National Center for Soybean
Biotechnology (X.-C.Z., X.W., S.F., J.W., M.L., H.T.N., G.S.)
and Division of Biochemistry, Department of Molecular Microbiology and
Immunology (G.S.), University of Missouri, Columbia, Missouri 65211;
and United States Department of Agriculture-Agricultural Research
Service and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (S.B.C.)
... Center. BAC sequences were annotated using the dicot species model and
Arabidopsis matrix of FGENESH (www.softberry.com). Annotated ...
Nature
443, 931 - 949 (26 Oct 2006)
Insights into social insects from the genome of the honeybee Apis mellifera
The Honeybee Genome Sequencing Consortium
...to produce a master gene list: the Official Gene Set (OGS). The component gene sets
were from NCBI, Ensembl, Softberry (Fgenesh), an evolutionarily conserved
core set and a set based on Drosophila orthologues (Supplementary...
PNAS
| October 24, 2006 | vol. 103 | no. 43 | 15794-15799
Vitamin K-dependent proteins in Ciona intestinalis,
a basal chordate lacking a blood coagulation cascade
John D. Kulman*, Jeff E. Harris*, Noriko Nakazawa, Michio Ogasawara, Masanobu Satake, and Earl W. Davie*,
*Department of Biochemistry, University of Washington, Seattle, WA 98195; Department of Biology, Faculty of Science, Chiba University, Chiba 263-8522, Japan; and Institute of Development, Aging, and Cancer, Tohoku University, Sendai 980-8575, Japan
... scaffolds. The resulting sequences were analyzed for probable intron/exon
boundaries with FGENESH (Softberry, Mount Kisco, NY). ...
TAG Theoretical and Applied Genetics
Volume 113, Number 6 / October, 2006 1147-1158
The barley serine/threonine kinase gene Rpg1 providing
resistance to stem rust belongs to
a gene family with five other members encoding kinase domains
R. Brueggeman 1 , T. Drader 2 and A. Kleinhofs 1, 2
(1) Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA
(2) School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4234, USA
... gene struc- tures were predicted by sequence comparison with the Rpg1 cDNA sequence
and using the FGENESH gene prediction program (http://www.softberry.com). ...
Annual Review of Phytopathology
Vol. 44: 337-366 (Volume publication date September 2006)
The Dawn of Fungal Pathogen Genomics
Jin-Rong Xu,1 You-Liang Peng,2 Martin B. Dickman,3 and Amir Sharon4
1Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
... at the Broad Institute, gene structures are predicted using the Calhoun annotation
system that is a combination of FGENESH (http://www.softberry.com),
FGENESH+ ...
Insect Molecular Biology
Volume 15 Issue 5 Page 597-602, October 2006
Expression of insulin pathway genes during the period of caste
determination in the honey bee, Apis mellifera
D. E. Wheeler, N. Buck, J. D. Evans
Department of Entomology, University of Arizona, Tucson AZ USA, USDA ARS, Bee Research Laboratory, Beltsville, MD 20705 USA
... Primers were designed based on cDNA sequences from the official gene list or on
the basis of FGENESH ( http:/ / www.softberry.com ) predictions of genomic ...
BMC Genomics.
2006; 7: 321
Quantitative analysis of cell-type specific gene expression in the
green alga Volvox carteri
Ghazaleh Nematollahi,#1 Arash Kianianmomeni,#1 and Armin Hallmann1
1Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitatsstr. 25, D-33615 Bielefeld, Germany
...Exon-intron prediction of Volvox genes was done using
FGENESH software (Softberry, Mount Kisco, NY) and by polypeptide
sequence comparisons with homologs from other organisms using ...
Developmental Biology
300 (2006) 2-8
Shedding genomic light on Aristotle's lantern
Erica Sodergren et al.,
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Alkek N1519, Houston, TX 77030, USA
...using software developed at Ensembl (Potter
et al., 2004; Sea Urchin Genome Sequencing Consortium,
2006) and installed at BCM-HGSC, NCBI (gnomon software;
Souvorov et al., 2004), Softberry (FgenesH software; Salamov
and Solovyev, 2000; Solovyev, 2001),...
Genetics.
2006 November; 174(3): 1493 - 1504.
Types and Rates of Sequence Evolution at the High-Molecular-Weight Glutenin Locus in Hexaploid Wheat and Its Ancestral Genomes
Yong Qiang Gu et al.,
United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, California 94710
...FGENESH (http://www.softberry.com/nucleo.html) and GENESCAN (http://genemark.mit.edu/GENESCAN.htm) were used for gene prediction...
DNA Sequence,
Volume 17, Issue 3 June 2006 , pages 223 - 230
Isolation and characterization of the RanGAP gene in the mosquito Aedes aegypti
Sung-Jae Cha a; Neil Lobo b; Becky Debruyn b; David W. Severson b
a Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Malaria Research Institute. Baltimore, MD. USA
b Department of Biological Sciences, Center for Tropical Disease Research and Training, University of Notre Dame. Notre Dame, IN. USA
... submitted to two gene finding programs: GENSCAN (http://genes.mit.edu/ GENSCAN.html)
using the vertebrate database and FGENESH (http://www.softberry.com/berry ...
Molecular Plant Pathology
Volume 7 Issue 6 Page 485-497, November 2006
The global nitrogen regulator, FNR1, regulates fungal nutrition-genes
and fitness during Fusarium oxysporum pathogenesis
HEGE HVATTUM DIVON, CARMIT ZIV, OLGA DAVYDOV, ODED YARDEN, ROBERT FLUHR
1Department of Plant Science, Weizmann Institute of Science, 76100 Rehovot, Israel
... The sequence was, in the Softberry gene prediction database ( http:/ /
www.softberry.com/ berry.phtml ; FGENESH), predicted to contain an open reading ...
Genetics.
2006 October; 174(2): 1017-1028.
Sequence Conservation of Homeologous Bacterial Artificial Chromosomes
and Transcription of Homeologous Genes in Soybean (Glycine max L. Merr.)
Jessica A. Schlueter,* Brian E. Scheffler, Shannon D. Schlueter,* and Randy C. Shoemaker‡1
*Department of Genetics, Developmental and Cellular Biology, Iowa State University, Ames, Iowa 50011, USDA-ARS MSA Genomics Laboratory, Stoneville, Mississippi 38776 and ‡USDA-ARS-CICGR, Ames, Iowa 50011
... Genscan with Arabidopsis thaliana-based parameters (Burge and Karlin 1997), FgeneSH
with Medicago truncatula-based parameters (http://www.softberry.com) and ...
Applied and Environmental Microbiology,
October 2006, p. 6527-6532, Vol. 72, No. 10
The Homologue of het-c of Neurospora crassa
Lacks Vegetative Compatibility Function in Fusarium proliferatum
Zoltan Kerenyi,1 Brigitta Olah,1,2 Apor Jeney,1 Laszlo Hornok,1,2 and John F. Leslie3*
Agricultural Biotechnology Center, Szent-Gyorgyi A. u. 4., H-2100 Godoll,
Hungary,
1 Department of Agricultural Biotechnology and Microbiology, Mycology Group,
Hungarian Academy of Sciences, Szent Istvan University, Pater K. u. 1., H-2103 Godoll,
Hungary,
2 Department of Plant Pathology, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, Kansas 66506-55023
... Sequence data were analyzed with the Lasergene software package (DNAStar Inc., Madison,
Wis.) and the FGENESH program (http://www.softberry.com). ...
Genetics
2006 November; 174(3): 1671 - 1683
Genetic Dissection of Intermated Recombinant Inbred Lines Using a New Genetic Map of Maize
Yan Fu et al.,
*Interdepartmental Genetics Graduate Program, Iowa State University, Ames, Iowa 50011, Department of Agronomy, Iowa State University, Ames, Iowa 50011
... 2004) alignments between genomic and EST sequences or predicted using FGENESH
(http://www.softberry.com) as described (Yao et al. 2005). ...
ChemBioChem
2006 Volume 7, Issue 1 , Pages 158 - 164
Reverse Prenyltransferase in the Biosynthesis of Fumigaclavine C in
Aspergillus fumigatus: Gene Expression, Purification, and Characterization of Fumigaclavine C Synthase FGAPT1
Inge A. Unsold, Shu-Ming Li, Priv. Doz. Dr. *
Eberhard-Karls-Universitat Tubingen, Pharmazeutische Biologie, Auf der Morgenstelle 8, 72076 Tubingen, Germany,
... FGENESH (Softberry, Inc., www.softberry.com/berry.phtml) and the DNASIS software
package (version 2.1: Hitachi Software Engineer- ing, San Bruno, CA) were used ...
Fungal Genetics and Biology
43 (2006) 316-325
Development of a Fusarium graminearum AVymetrix GeneChip for
proWling fungal gene expression in vitro and in planta
Ulrich Guldener et al.,
Technische Universität Munchen, Chair of Genome Oriented Bioinformatics, Center of Life and Food Science,
D-85350 Freising-Weihenstephan, Germany
... to the automatically pre- dicted set from the Broad Institute, a second automatic
gene call set was developed at MIPS using FGENESH (www.softberry.com) with a ...
The Journal of Clinical Endocrinology & Metabolism
2006 Vol. 91, No. 11 4587-4592
Identification of Three Novel Mutations in the GATA3
Gene Responsible for Familial Hypoparathyroidism and Deafness
in the Chinese Population
Wei-Yih Chiu, Huan-Wen Chen, Hwei-Wen Chao, Lee-Tzong Yann and Keh-Sung Tsai
Departments of Laboratory Medicine (W.-Y.C., H.-W.Cha, K.-S.T.) and Internal Medicine (W.-Y.C., L.-T.Y, K.-S.T.), National Taiwan University Hospital, Taipei 100, Taiwan; and Department of Internal Medicine (H.-W.Che), Lo-Tung Pohai Hospital, Ilan 256, Taiwan
... is useful. We used the FGENESH program (www.softberry.com) based on the
consensus sequence of exon-intron junctions (ag ... gt rule ...
CURRENT SCIENCE
VOL. 91, NO. 4, 25 AUGUST 2006 510-515
Bioinformatics approach toward
identification of candidate genes for
zinc and iron transporters in maize
R. S. Chauhan
Bioinformatics Centre, Advanced Centre of Hill Bioresources and
Biotechnology, CSK HP Agricultural University,
Palampur 176 062, India
... using gene prediction algorithms of FGenesH 18 (http://www.softberry.com/
berry.phtml? topic= fgenesh&group=programs&subgroup=gfind ...
Acta Biochimica et Biophysica Sinica
Volume 38, Number 11, November 2006 , pp. 812-820(9)
Sequencing and Analysis of a Genomic Fragment
Provide an Insight into the Dunaliella viridis Genomic Sequence
SUN, Xiao-Ming et al.,
Shanghai Key Laboratory of Bio-energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
... Gene prediction was carried out using GENSCAN (http://genes.mit.edu/GENSCAN.
html) and FGENESH (http://www.softberry.com/berry.html). ...
Functional & Integrative Genomics
Volume 6, Number 4 / October, 2006 pp. 338-341
Drought tolerance genes in rice
Huazong Zeng, Yang Zhong and Lijun Luo
Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, 200433, People’s Republic of China
Shanghai Agro-Biological Gene Center, Shanghai, 201106, People’s Republic of China
... ncbi.nih.gov/) through BLAST. After this, Fgenesh soft- ware (http://www.
softberry.com) was used to predict candidate genes. All ...
Genome
Volume 49, Number 3, 1 March 2006, pp. 209-218(10)
Molecular structure and organization of the wheat genomic manganese superoxide dismutase gene
Baek, Kwang-Hyun; Skinner, Daniel Z.; Ling, Peng; Chen, Xianming
... softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind; Salamov
and Solovyev 2000) and GeneScan (http://genes.mit.edu/GENSCAN. ...
Nucleic Acids Research
2006 34(17):4685-4701
Organization of chromosome ends in the rice blast
fungus, Magnaporthe oryzae
Cathryn Rehmeyer et al.,
Department of Plant Pathology, University of Kentucky Lexington, KY 40546 USA
... The masked sequences were then used for gene prediction with Fgenesh (67) trained
on M.oryzae sequences (Softberry, www.softberry.com). ...
TAG Theoretical and Applied Genetics
Volume 113, Number 5 / September, 2006 pp.875-883
Identification and fine mapping of AvrPi15,
a novel avirulence gene of Magnaporthe grisea
Jun-Hong Ma et al.,
Laboratory of Plant Resistance and Genetics, College of Resources and Environmental Sciences, South China Agricultural University, Guangzhou, 510642, China
... out with the CAG markers, which were developed based on the sequence of the candidate
genes predicted using the gene annotation system, Softberry FGENESH ...
The Plant Cell
18:1339-1347 (2006)
Sequence-Level Analysis of the Diploidization Process in the Triplicated FLOWERING LOCUS C Region of Brassica rapa
Yang et al.,
Brassica Genomics Team, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Korea
... Gene annotation was achieved using the web-based gene prediction program
FGENESH Arabidopsis (http://www.softberry.com/berry.phtml). ...
Genome Research
16:618-626, 2006
Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice
He et al.,
State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
... 1997 Go) programs. Sequence analysis and gene prediction were performed by using
the gene-finding programs FGENESH (http://www.softberry.com/berry.phtml). ...
Molecular Genetics and Genomics
Volume 275, Number 5 / May, 2006 pp. 450-459
Master: a novel family of PIF/Harbinger-like transposable elements identified in carrot (Daucus carota L.)
Dariusz Grzebelus, Yuan-Yeu Yau and Philipp W. Simon
Department of Genetics, Plant Breeding and Seed Science, Agricultural University of Krakow, 31-425 Krakow, Poland
USDA-ARS Vegetable Crops Research Unit and Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706, USA
... ORF and exon/intron localization were predicted using GenScan (URL: http://www.genes.
mi- t.edu/GENSCAN.html) and FGenesh (URL: http:// www.softberry.com). ...
Planta
Volume 223, Number 6 / May, 2006 pp. 1134-1144
Identification and characterization of an Arabidopsis homogentisate phytyltransferase paralog
Venkatesh et al.
Monsanto Company, 800 N. Lindbergh Boulevard, St. Louis, MO 63167, USA
... http://hmmer.wustl.edu/). Gene prediction software FGENESH was procured
from Softberry Inc., NY, USA. Dicot model provided with ...
Development Genes and Evolution
Volume 216, Number 4 / April, 2006 pp. 198-208
A comparative study of sperm morphology, cytology and activation in
Caenorhabditis elegans, Caenorhabditis remanei and Caenorhabditis briggsae
Geldziler et al.
Department of Genetics, Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
... The genome sequence around the sequence thus identified was used as an input for
the gene prediction algorithms FGeneSH (http://www.softberry.com/berry. ...
Mol. Ecol.
Volume 15 Issue 5 Page 1367 -1378. April 2006
Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa
Gilchrist et al.
Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
... Gene models were predicted using fgenesh (Salamov & Solovyev 2000) through
the Softberry website ( http:/ / www.softberry.com ). ...
Genome Research
16:618-626, 2006
Haplotype variation in structure and expression of a gene cluster associated with a quantitative
trait locus for improved yield in rice
Guangming He et al.
1 State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China;
... 1997 Go) programs. Sequence analysis and gene prediction were performed by using
the gene-finding programs FGENESH (http://www.softberry.com/berry.phtml). ...
The Plant Cell
18:1339-1347 (2006)
Sequence-Level Analysis of the Diploidization Process in the Triplicated FLOWERING LOCUS C
Region of Brassica rapa[W],[OA]
Tae-Jin Yanga et al.
a Brassica Genomics Team, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Korea
... Gene annotation was achieved using the web-based gene prediction program
FGENESH Arabidopsis (http://www.softberry.com/berry.phtml). ...
Medical Mycology
Publisher: Taylor & Francis
Issue: Volume 44, Number 3 / May 2006
Pages: 211 - 218
The role of the sakA (Hog1) and tcsB (sln1) genes in the oxidant adaptation of Aspergillus fumigatus
Chen Du A1, Jacqueline Sarfati A2, J-P Latge A2, Richard Calderone A1
A1 Department of Microbiology & Immunology, Georgetown University Medical Center, Washington, DC, USA
A2 Aspergillus Unit, Institut Pasteur, Paris, France
... tcsB gene and phenotype of the deletion mutant DNA sequence analysis of tcsB
(gene-finding software FGENESH. WWW.softberry.com) revealed a long Fig. ...
Molecular Genetics and Genomics
Issue: Volume 275, Number 5
Date: May 2006
Pages: 504 - 511
A complete physical map of a wild beet (Beta procumbens) translocation in sugar beet
Daniela Schulte1, Daguang Cai1, Michael Kleine1, 2, Longjiang Fan1, 3, Sheng Wang1, 3 and Christian Jung1
(1) Plant Breeding Institute, Christian-Albrechts-University Kiel, Olshausenstr. 40, 24098 Kiel, Germany
(2) Present address: PLANTON GmbH, Am Kiel-Kanal 44, 24106 Kiel, Germany
(3) Institute of Bioinformatics and Institute of Crop Science, Zhejiang University, 310029 Hangzhou, China
... An ab initio ORF-analysis with the FgeneSH program on http://www.sun1.softberry.
com was performed to iden- tify putative coding regions using the A. thaliana ...
Molecular Genetics and Genomics
Issue: Volume 275, Number 5
Date: May 2006
Pages: 450 - 459
Master: a novel family of PIF/Harbinger-like transposable elements identified in carrot (Daucus carota L.)
Dariusz Grzebelus1, Yuan-Yeu Yau2, 3, 4 and Philipp W. Simon2
(1) Department of Genetics, Plant Breeding and Seed Science, Agricultural University of Krakow, 31-425 Krakow, Poland
... ORF and exon/intron localization were predicted using GenScan (URL: http://www.genes.
mi- t.edu/GENSCAN.html) and FGenesh (URL: http:// www.softberry.com). ...
Development Genes and Evolution
Issue: Volume 216, Number 4
Date: April 2006
Pages: 198 - 208
A comparative study of sperm morphology, cytology and activation in
Caenorhabditis elegans, Caenorhabditis remanei and Caenorhabditis briggsae
Brian Geldziler1, Indrani Chatterjee1, Pavan Kadandale1, Emily Putiri1, Rajesh Patel2 and Andrew Singson1
(1) Department of Genetics, Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
(2) Department of Pathology, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
... The genome sequence around the sequence thus identified was used as an input for
the gene prediction algorithms FGeneSH (http://www.softberry.com/berry. ...
Planta
Issue: Volume 223, Number 6
Date: May 2006
Pages: 1134 - 1144
Identification and characterization of an Arabidopsis homogentisate phytyltransferase paralog
Tyamagondlu V. Venkatesh1, Balasulojini Karunanandaa1, Daniel L. Free2, Jeannie M. Rottnek2, Susan R. Baszis2 and Henry E. Valentin3
(1) Monsanto Company, 800 N. Lindbergh Boulevard, St. Louis, MO 63167, USA
... http://hmmer.wustl.edu/). Gene prediction software FGENESH was procured
from Softberry Inc., NY, USA. Dicot model provided with ...
TAG Theoretical and Applied Genetics
Issue: Volume 112, Number 6
Date: April 2006
Pages: 1179 - 1191
Molecular cytogenetics and DNA sequence analysis of an apomixis-linked BAC in
Paspalum simplex reveal a non pericentromere location and partial microcolinearity with rice
Ornella Calderini1, Song B. Chang2, 6, Hans de Jong2, Alessandra Busti1, Francesco Paolocci1, Sergio Arcioni1, Sacco C. de Vries3, Marleen H. C. Abma-Henkens4, Rene M. Klein Lankhorst4, Iain S. Donnison5 and Fulvio Pupilli1
(1) Institute of Plant Genetics CNR, Perugia via della madonna alta 130, 06128 Perugia, Italy
... Gene structure and predicted protein sequences were obtained from assembled contigs
using the FGENESH program at the SoftBerry site (http://www.softberry.com ...
ChemBioChem
2006, Volume 7, Issue 1 , Pages 158 - 164
Reverse Prenyltransferase in the Biosynthesis of Fumigaclavine C in Aspergillus fumigatus: Gene Expression, Purification, and Characterization of Fumigaclavine C Synthase FGAPT1
Inge A. Unsold, Shu-Ming Li, Priv. Doz. Dr.
Eberhard-Karls-Universitat Tubingen, Pharmazeutische Biologie, Auf der Morgenstelle 8, 72076 Tubingen, Germany, Fax: (+49) 7071-29-5250;
... FGENESH (Softberry, Inc., www.softberry.com/berry.phtml) and the DNASIS software
package (version 2.1: Hitachi Software Engineer- ing, San Bruno, CA) were used ...
Genetics
Genetics, Vol. 173, 131-149, May 2006
Searching for neuronal left/right asymmetry:
Genome wide analysis of nematode receptor-type guanylyl cyclases
Christopher O. Ortiz et.al.,
Howard Hughes Medical Institute
Department of Biochemistry and Molecular Biophysics
Columbia University Medical Center
701 W.168th Street
New York, NY 10032
... Wormbase WS149), we suspected that C. briggsae genes may have been incorrectly
predicted. We therefore ran the FGENESH program at www.softberry.com (S ALAMOV ...
Genome Biology
2006, 7:R16 doi:10.1186/gb-2006-7-2-r16
The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae
Michael R Thon et al.,
Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
The gene prediction program FGENESH
(Softberry Corporation, Mount Kisco, NY, USA) trained to predict M. oryzae genes [3] was used to identify 1,151 putative gene coding sequences.
Genetics
Published Articles Ahead of Print, published on February 19, 2006 as 10.1534/genetics.105.054791
Distribution of microsatellites in the genome of Medicago truncatula: A resource of genetic
markers that integrate genetic and physical maps.
Jeong-Hwan Mun et al.,
Department of Plant Pathology, University of California, Davis, CA, USA.
... Gene-coding regions were predicted in M. truncatula using the eudicot version of
FGENESH (www.softberry.com). BAC-end sequences were divided into gene- ...
Theor Appl Genet
(2006)
DOI 10.1007/s00122-005-0201-2
Development of four phylogenetically-arrayed BAC libraries and sequence
of the APA locus in Phaseolus vulgaris
James Kami, Vale´ rie Poncet, Vale´ rie Geffroy,
Paul Gepts
Department of Plant Sciences, Section of Crop and Ecosystem
Sciences, University of California, Mailstop 1, 1 Shields Avenue,
Davis, CA 95616-8780, USA
... www.genes.cs.wustl.edu/), and FGENESH (http:// www.softberry.com/; trained with
Nicotiana tabacum, Medicago truncatula, Dicot or Monocot). ...
Molecular Ecology
15 (5), 1367-1378.
- April 2006
Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa
ERIN J. GILCHRIST et al.,
Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
... Gene models were predicted using fgenesh (Salamov & Solovyev 2000) through
the Softberry website ( http:/ / www.softberry.com ). ...
Applied and Environmental Microbiology
, March 2006, p. 1793-1799, Vol. 72, No. 3
Characterization of Two Polyketide Synthase Genes Involved in Zearalenone Biosynthesis in Gibberella zeae
Iffa Gaffoor1 and Frances Trail1,2
Departments of Plant Biology,1 Plant Pathology, Michigan State University, East Lansing, Michigan 488242
... portions of the sequence. Using this complete sequence, FGENESH software
(http://www. softberry. com) with organism-specific parameters ...
Medical Mycology
Volume 44, Number 3 / May 2006
Pages: 211 - 218
The role of the sakA (Hog1) and tcsB (sln1) genes in the oxidant adaptation of Aspergillus fumigatus
Chen Du A1, Jacqueline Sarfati A2, J-P Latge A2, Richard Calderone A1
A1 Department of Microbiology & Immunology, Georgetown University Medical Center, Washington, DC, USA
A2 Aspergillus Unit, Institut Pasteur, Paris, France
... tcsB gene and phenotype of the deletion mutant DNA sequence analysis of tcsB
(gene-finding software FGENESH. WWW.softberry.com) revealed a long Fig. ...
Genetics
Vol. 172, 2491-2499, April 2006
Tracing Nonlegume Orthologs of Legume Genes Required for Nodulation and Arbuscular Mycorrhizal Symbioses
Hongyan Zhu1, Brendan K. Riely2, Nicole J. Burns3, Jean-Michel Ané3
1Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546
... GenBank database. Gene prediction was performed by FGENESH (http://www.
softberry.com/berry.phtml?topic=gfind). Sequence alignments ...
TAG Theoretical and Applied Genetics
Issue: Volume 112, Number 4
Date: February 2006
Pages: 618 - 626
Structural variation and evolution of a defense-gene cluster in natural populations of Aegilops tauschii
Steven A. Brooks1, 3, Li Huang2, Marie N. Herbel2, Bikram S. Gill2, Gina Brown-Guedira1 and John P. Fellers1
(1)Plant Science and Entomology Unit, Department of Plant Pathology, USDA-ARS, Manhattan, KS 66506, USA
... FGENESH 1.1 (http:// www.softberry.com) was used for coding sequence (CDS)
prediction with monocot genomic DNA param- eters. Putative ...
Plant Physiology
, March 2006, Vol. 140, pp. 998-1008
Point Mutations with Positive Selection Were a Major Force during the Evolution of a Receptor-Kinase Resistance Gene Family of Rice
Xinli Sun, Yinglong Cao and Shiping Wang
National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
... 1997 Go). The gene prediction programs used were GENSCAN (Burge and Karlin,
1997 Go) and FGENESH (http://www.softberry.com). The ...
Mol Gen Genomics
Volume 275, Number 5 / May, 2006 pp. 504-511
A complete physical map of a wild beet ( Beta procumbens) translocation
in sugar beet
Daniela Schulte, Daguang Cai, Michael Kleine,
Longjiang Fan, Sheng Wang, Christian Jung
Plant Breeding Institute, Christian-Albrechts-University Kiel,
Olshausenstr. 40, 24098 Kiel, Germany
... An ab initio ORF-analysis with the FgeneSH program on http://www.sun1.softberry.
com was performed to iden- tify putative coding regions using the A. thaliana ...
Molecular Microbiology
2006, 60 (1), 67-80
Lost in the middle of nowhere: the AvrLm1 avirulence gene of the Dothideomycete Leptosphaeria maculans
Lilian Gout 1 et al.,
Phytopathologie et Methodologies de la Detection, INRA, F-78026 Versailles, France.
... genscan ( http:/ / genes.mit.edu/ GENSCAN.html ) was used with vertebrate and
Arabidopsis settings and fgenesh ( http:/ / www.softberry.com ) was set with N ...
J Gen Virol
87 (2006), 311-322
Characterization and transcriptional analysis of protein tyrosine phosphatase genes and an ankyrin
repeat gene of the parasitoid Glyptapanteles indiensis polydnavirus in the parasitized host
D. E. Gundersen-Rindal and M. J. Pedroni
US Department of Agriculture, Agricultural Research Service, Insect Biocontrol Laboratory, Bldg 011A, Room 214, BARC West, Beltsville, MD 20705, USA
... nih.gov/gorf/gorf.html (only large ORFs are shown)], FGENESH [ab initio ... gambiae and
Apis mellifera insect gene parameters; http://www.softberry.com (Salamov & ...
Current Biology
2005, Volume 15, Issue 16, Pages 1508-15
Select a website below to get this article
Causier et al.,
... 25], GeneMark.hmm (http://opal.biology.gatech.edu/genemark/eukhmm.cgi) [26] (each
with the Arabidopsis dataset), and FGENESH (http://www.softberry.com/) (with ...
Plant Molecular Biology
Volume 58, Number 6 / August, 2005, pp. 809-822
The Medicago truncatula SUNN Gene Encodes a CLV1-like Leucine-rich Repeat Receptor Kinase that Regulates Nodule Number and Root Length
Elise et al.,
(1) Department of Genetics, Biochemistry and Life Science Studies, Clemson University, 100 Jordan Hall, Clemson, SC 29634, USA
(2) Laboratoire des Interactions Plantes-Microorganismes, Unité Mixte de Recherche, CNRS-INRA, 31326 Castanet-Tolosan cédex, France
... Genes in this region were predicted using FGENESH (http:// www.softberry.com) (Salamov
and Solovyev, 2000) using parameters for the M. truncatula genome, the ...
TAG Theoretical and Applied Genetics
Volume 111, Number 3 / August, 2005, pp. 467-478
Toward closing rice telomere gaps: mapping and sequence characterization of rice subtelomere regions
Yang et al.,
(1) Brassica Genomics Team, National Institute of Agricultural Biotechnology, RDA, Suwon, 441-707, Korea
(2) Arizona Genomics Institute, University of Arizona, 303 Forbes building, Tucson, AZ 85721, USA
... while the detection of putative genes was analyzed using sev- eral web-based gene
prediction programs including: FGENE-SH MONOCOT (http://www.softberry.com/ber ...
Chromosoma
Volume 114, Number 2 / July, 2005, pp. 103-117
In-depth sequence analysis of the tomato chromosome 12 centromeric region: identification of a large CAA block and characterization of pericentromere retrotranposons
Yang et al.,
(1) Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB), RDA, Suwon, 441-707, South Korea
(2) Arizona Genomics Institute, 303 Forbes building, University of Arizona, Tucson, AZ 85721, USA
... Gene an- notation was achieved using several web-based gene pre- diction programs
such as FGENE-SH Arabidopsis (http:// www.softberry.com/berry.phtml ...
Journal of Molecular Evolution
Volume 61, Number 4 / October, 2005, pp. 559-569
Plant Photoreceptors: Phylogenetic Overview
Patricia Lariguet1 and Christophe Dunand1
(1) Department of Plant Biology, University of Geneva, Quai Ernest Ansermet 30, Geneva 4, CH-1211, Switzerland
... quences were analyzed for the presence of the gene with different programs such
as FGenesh (http://www.softberry.com/ber- ry.phtml) and GenScan (http://genes ...
Journal of Molecular Evolution
Volume 60, Number 5 / May, 2005, pp. 615-634
Structure, Evolution, and Expression of the Two Invertase Gene Families of Rice
Xuemei Ji1, 2, Wim Van den Ende3, Andre Van Laere3, Shihua Cheng2 and John Bennett 1
1) Plant Breeding, Genetics and Biochemistry Division, International Rice Research Institute, DAPO, 7777, Metro Manila, Philippines
(2) Chinese National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, Zhejiang, 310006, China
... supplemented the above methods with the use of Genscan (http://genes.mit.edu/
GENSCAN.html) (Burge and Karlin 1997) and FGENESH (http://www.softberry.ru/berry ...
Genetics
Published Articles Ahead of Print: May 6, 2005, Copyright © 2005
doi:10.1534/genetics.105.041616
Centric regions of soybean (Glycine max L. Merr.) chromosomes consist of retroelements and tandemly repeated DNA and are structurally and evolutionarily labile
Lin et al.,
1 Purdue University
2 USDA-ARS-CICGR, and Department of Agronomy
3 University of Minnesota
... Fifteen potential genes were found on the BAC using FGENESH (http://www.softberry.
com/berry.phtml) (Table 2). Three of the fifteen (4-6) ...
TAG Theoretical and Applied Genetics
Volume 111, Number 6 / October, 2005, pp. 1080-1086
Delimitation of the rice wide compatibility gene S5n to a 40-kb DNA fragment
Qiu et al.,
(1) National Key Laboratory of Crop Genetic Improvement, and National Center of Plant Gene Research-Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
... Gene prediction analysis of the 40-kb DNA fragment using FGENSH (http://www.softberry.
com) identified five putative open reading frames (ORFs; Fig. 2). Both ...
Molecular Genetics and Genomics
Volume 274, Number 6 / December, 2005, pp. 569-578
High-resolution mapping, cloning and molecular characterization of the Pi-k h gene of rice, which confers resistance to Magnaporthe grisea
Sharma et al.,
(1) National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
... The 143,537 bp region of Nipponbare identified by physical mapping was then analysed
with FGENESH software (http://www.softberry.com) to detect putative genes. ...
Genetics
2005 July; 170(3): 1221–1230.
doi: 10.1534/genetics.105.041616.
Pericentromeric Regions of Soybean (Glycine max L. Merr.) Chromosomes Consist of Retroelements and Tandemly Repeated DNA and Are Structurally and Evolutionarily Labile
Lin et al.,
*Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
†Purdue University Genomics Core, Department of Horticulture, Purdue University, West Lafayette, Indiana 47907
... Fifteen potential genes were found on the BAC using FGENESH (http://www.softberry.
com/berry.phtml) (Table 2). Three of the 15 (4-6) were derived from either ...
Genomics
Volume 85, Issue 6, June 2005, Pages 666-678
Biosilica formation in spicules of the sponge Suberites domuncula: Synchronous expression of a gene cluster
Schroder et al.,
aInstitut fur Physiologische Chemie, Abteilung Angewandte Molekularbiologie, Johannes Gutenberg-Universitat, Duesbergweg 6, D-55099 Mainz, Germany
... Four open reading frames (ORFs) were predicted using the program FGENESH ("softberry"):
putative ankyrin repeat protein ANKrp_SUBDO (SDANKrp), silicatein ...
Genetics
2005 February; 169(2): 891–906.
doi: 10.1534/genetics.104.034629.
Structure and Evolution of the r/b Chromosomal Regions in Rice, Maize and Sorghum
Zuzana Swigonova,* Jeffrey L. Bennetzen,†1 and Joachim Messi
*Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020
†Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392
... Finnzyme, Helsinki). Sequence analysis: Genes predicted by FGENESH
(http://www.softberry.com/berry.phtml? topic=gfind&prg=FGENESH ...
Genetics
2005 March; 169(3): 1403–1414.
doi: 10.1534/genetics.104.035972.
Gene Clusters for Insecticidal Loline Alkaloids in the Grass-Endophytic Fungus Neotyphodium uncinatum
Martin J. Spiering,* Christina D. Moon,*1 Heather H. Wilkinson,† and Christopher L. Schardl*2
*Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546-0312
†Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843-2132
... with the search parameters for the N. crassa genome, genomic DNA sequences were
entered into the FGENESH gene prediction program (http://www.softberry.com/berry ...
Genetics
2005 July; 170(3): 1209–1220.
doi: 10.1534/genetics.105.040915.
DNA Rearrangement in Orthologous Orp Regions of the Maize, Rice and Sorghum Genomes
Jianxin Ma,*† Phillip SanMiguel,‡ Jinsheng Lai,§ Joachim Messing,§ and Jeffrey L. Bennetzen*†1
Department of Genetics, University of Georgia, Athens, Georgia 30602
†Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
... Sequence analysis and annotation: Gene-finding programs FGENESH (http://www.softberry.
com/berry.phtml?topic=gfind&prg=FGENESH) with the monocot training set ...
PNAS
August 23, 2005 vol. 102 no. 34 12282-12287
Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes
Yan Fu et al.,
*Interdepartmental Genetics Graduate Program, §Interdepartmental Bioinformatics and Computational Biology Graduate Program, **L. H. Baker Center for Bioinformatics and Biological Statistics
... fgenesh (Softberry, Mount Kisco, NY) was used for ab initio gene prediction with
monocot parameters and the GC option that uses all potential GC donor splice ...
PNAS
December 27, 2005 vol. 102 no. 52 19243-19248
Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat
Devos et al.,
Departments of *Crop and Soil Sciences, †Plant Biology, and §Genetics, University of Georgia, Athens, GA 30602
... The gene prediction program fgenesh, with the monocot (maize, rice, wheat, and barley)
training set (www.softberry.com), was used to predict genes. ...
Eukaryotic Cell
November 2005, p. 1926-1933, Vol. 4, No. 11
Functional Analysis of the Polyketide Synthase Genes in the Filamentous Fungus Gibberella zeae (Anamorph Fusarium graminearum)
Gaffoor et al.,
Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824,1 Mycotoxin Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, Illinois 61604,2
... Ab initio gene identification was accomplished using FGENESH (http://www.softberry.
com) with organism-specific parameters for Neurospora crassa (12). ...
Cytokine
Volume 32, Issue 5, 7 December 2005, Pages 219-225
Expression of nine-banded armadillo (Dasypus novemcinctus) interleukin-2 in E. coli
Adams et al.,
Laboratory Research Branch National Hansen's Disease Programs, Louisiana State University, School of Veterinary Medicine, Skip Bertman Drive, Baton Rouge, LA 70803, USA
... The genomic sequence was submitted to FGENESH (http://www.softberry.com) to derive
a putative cDNA and a corresponding translation for the putative amino acid ...
Comparative and Functional Genomics
Volume 6 (2005), Issue 3, Pages 138-146doi:10.1002/cfg.465
The Korea Brassica Genome Project: a Glimpse of the Brassica Genome Based on Comparative Genome Analysis With Arabidopsis
Tae-Jin Yang et al.,
1National Institute of Agricultural Biotechnology (NIAB), 224 Suinro Gwonseon-gu, Gyeonggi-do, Suwon 441–707, Korea
2Chungnam National University, Gungdong 220, Chungnam, Daejeon 305–764, Korea
... Gene annotation was achieved using several web based gene prediction programs,
eg FGENE-SH Arabidopsis (http://www.softberry.com/berry. ...
Plant Molecular Biology
Volume 59, Number 1 / September, 2005, pp.191-203
Transcription Factors in Rice: A Genome-wide Comparative Analysis between Monocots and Eudicots
Xiong et al.,
(1) Present address: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
... BGI) (Yu et al., 2002) (http://www.genomics.org.cn/) and the genes were predicted
using FGENESH (Salamov and Solovyev, 2000) (http://www.softberry.com/). ...
Molecular Biology and Evolution
2005 22(10):2084-2089; doi:10.1093/molbev/msi202
MUSTANG Is a Novel Family of Domesticated Transposase Genes Found in Diverse Angiosperms
Rebecca K. Cowan, Douglas R. Hoen, Daniel J. Schoen and Thomas E. Bureau
McGill University, Biology Department, Montreal, Quebec H3A 1B1, Canada
... through AP006877 and National Center for Biotechnology Information [NCBI] accession
number AE016959), predicted using FGENESH (http://www.softberry.com/berry ...
Plant Molecular Biology
Issue: Volume 57, Number 3 Date: February 2005 Pages: 445 - 460
Evaluation of five ab initio gene prediction programs for the discovery of maize genes
Hong Yao1, 4 et al
Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, 50011-3650, USA.
ABSTRACT
Five ab initio programs (FGENESH, GeneMark.hmm, GENSCAN, GlimmerR and Grail) were evaluated for their accuracy in predicting maize genes. Two of these programs, GeneMark.hmm and GENSCAN had been trained for maize; FGENESH had been trained for monocots (including maize), and the others had been trained for rice or Arabidopsis. Initial evaluations were conducted using eight maize genes (gl8a, pdc2, pdc3, rf2c, rf2d, rf2e1, rth1, and rth3) of which the sequences were not released to the public prior to conducting this evaluation. The significant advantage of this data set for this evaluation is that these genes could not have been included in the training sets of the prediction programs. FGENESH yielded the most accurate and GeneMark.hmm the second most accurate predictions. The five programs were used in conjunction with RT-PCR to identify and establish the structures of two new genes in the a1-sh2 interval of the maize genome. FGENESH, GeneMark.hmm and GENSCAN were tested on a larger data set consisting of maize assembled genomic islands (MAGIs) that had been aligned to ESTs. FGENESH, GeneMark.hmm and GENSCAN correctly predicted gene models in 773, 625, and 371 MAGIs, respectively, out of the 1353 MAGIs that comprise data set 2.
Nature
434, 980-986 (21 April 2005)
The genome sequence of the rice blast fungus Magnaporthe grisea
Dean et al.,
Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina 27695, USA
School of Biological and Chemical Sciences, University of Exeter, Washington Singer Laboratories, Exeter EX4 4QG, UK
...Gene predictions were performed using FGENESH/FGENESH1 + trained on M. grisea sequences (SoftBerry) and GENEWISE (Sanger Center) and validated against 65 characterized M. grisea genes. Additional information and gene identification...
Nature
436, 793 - 800 (11 Aug 2005)
The map-based sequence of the rice genome
International Rice Genome Sequencing Project
...the remaining centromere gaps. Annotation and bioinformatics Gene models were predicted using FGENESH (http://www.softberry.com/berry.phtml?topic = fgenesh) using the monocot trained matrix on the native and repeat-masked...
Nature Genetics
37 997 - 1002 (01 Sep 2005) Letters
Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize
Morgante et al.,
1 Dipartimento di Scienze Agrarie ed Ambientali, Universita' di Udine, Via delle Scienze 208, 33100 Udine, Italy.
2 DuPont Crop Genetics Research, DuPont Experimental Station Building E353, Wilmington, Delaware 19880-353, USA.
...at http://www.girinst.org/~vladimir/RC/Data1.htm. We obtained FGENSH splicing site predictions from http://www.softberry.com/berry.phtml. Primer3 is available at http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi. Note:...
European Journal of Plant Pathology
Issue: Volume 112, Number 1 Date: May 2005 Pages: 23 - 29
Leptosphaeria maculans, a fungal pathogen of Brassica napus, secretes a subtilisin-like serine protease
Leanne M. Wilson and Barbara J. Howlett
1 School of Botany, The University of Melbourne, Parkville, Victoria, 3010, Australia
... DNA and cDNA sequences were compared to identify intron positions, which confirmed those predicted by FGENESH gene prediction software (www.softberry.com). ...
Current Genetics
Issue: Volume 47, Number 5 Date: May 2005 Pages: 307 - 315
During attachment Phytophthora spores secrete proteins containing thrombospondin type 1 repeats
Andrea V. Robold1 and Adrienne R. Hardham1
(1) Plant Cell Biology Group, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia
... info.html). The DNA sequence was searched for introns using the soft- ware program FGENESH (http://www.softberry. com/berry.phtml ...
Microbiology
151 (2005), 1499-1505
Overproduction, purification and characterization of FgaPT2, a dimethylallyltryptophan synthase from Aspergillus fumigatus
Inge A. Unsold and Shu-Ming Li
Pharmazeutische Biologie, Pharmazeutisches Institut, Eberhard-Karls-Universitat Tubingen, Auf der Morgenstelle 8, 72076 Tubingen, Germany
... FGENESH (Softberry; www.softberry.com/berry.phtml) and the DNASIS software package (version 2.1; Hitachi Software Engineering) were used for intron prediction ...
Eukaryotic Cell
March 2005, p. 526-535, Vol. 4, No. 3
Sex-Specific Homeodomain Proteins Sxi1a and Sxi2a Coordinately Regulate Sexual Development in Cryptococcus neoformans
Christina M. Hull,1, Marie-Josee Boily,1 and Joseph Heitman1,2*
Department of Molecular Genetics and Microbiology,1 the Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina2
... Sequence manipulations. Splice predictions of candidate gene sequences for SXI2a were facilitated with a Softberry algorithm (www.softberry.com). ...
New Phytologist
167 (1), July 2005, 239-247.
Identification of perennial ryegrass (Lolium perenne (L.)) and meadow fescue (Festuca pratensis (Huds.)) candidate orthologous sequences to the rice Hd1(Se1) and barley HvCO1 CONSTANS-like genes through comparative mapping and microsynteny
P. Armstead, L. Skot, L. B. Turner, K. Skot, I. S. Donnison, M. O. Humphreys and I. P. King
... Predictions of mRNA and protein sequences were carried out using FGENESH and
FGENESH+ software ( http:/ / www.softberry.com/ berry.phtml ). ...
Plant Physiology
May 2005, Vol. 138, pp. 38-46
BIOINFORMATICS-PLANT DATABASES
Databases and Information Integration for the Medicago truncatula Genome and Transcriptome1
Steven B. Cannon et al
Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (S.B.C., X.W., E.K.S.C., J.V., J.M., N.D.Y.)
... Annotation involves a multi-institution pipeline, relying on Medicago-trained FGENESH
(Salamov and Solovyev, 2000 ) predictions, the EuGene (Foissac et al ...
Plant Physiology
May 2005, Vol. 138, pp. 18-26
BIOINFORMATICS-PLANT DATABASES
The Institute for Genomic Research Osa1 Rice Genome Annotation Database1
Qiaoping Yuan et al
The Institute for Genomic Research, Rockville, Maryland 20850
... The ab initio gene finders used in the rice EGC pipeline include FGENESH (monocot
matrix; Salamov and Solovyev, 2000 ), GeneMark.hmm (rice matrix; Lukashin and ...
Genome Research
15:577-582, 2005
Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions
Chaochun Wei1 et al.
1 Laboratory for Computational Genomics and Department of Computer Science and Engineering, Washington University, St. Louis, Missouri 63130, USA
... Finally, we compared TWINSCAN with two other gene-prediction systems that have recently
been developed for nematodes-FGENESH (Salamov and Solovyev 2000 ...
Plant Physiology
April 2005, Vol. 137, pp. 1174-1181
UPDATE ON SEQUENCING MEDICAGO TRUNCATULA AND LOTUS JAPONICUS
Sequencing the Genespaces of Medicago truncatula and Lotus japonicus1
Nevin D. Young et al
Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (N.D.Y., S.B.C.)
... (These estimates are based on FGENESH predictions [Salamov and Solovyev, 2000] using a Mt-trained matrix, retaining peptides with a BLASTP match at 10e-4 to the UniProt NREF100 database of peptides [Apweiler et al., 2004]. This estimate for Lj differs from the published value of 1 gene per 10.1 kb [Asamizu et al., 2003a] due to the use here of the FGENESH gene-calling algorithm so Mt and Lj could be compared directly.)...
...This estimate increases to 6,500 when Lj genes are predicted by the Mt-trained FGENESH algorithm described earlier...
International Journal of Cancer
Volume 109, Issue 1 , Pages 71 - 75
Candidate regions of tumor suppressor locus on chromosome 9q31.1 in gastric cancer
Naoto Kakinuma 1 et al
1Novartis Pharma Tsukuba Research Institute, Ibaraki, Japan
2Laboratory of Molecular and Genetic Information, Institute for Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan
3Second Department of Surgery, Gunma University School of Medicine, Gunma, Japan
... predict the genes between D9S277 and D9S127 in 9q31.1, the gene prediction tools
also in the UCSC Genome Browser having Acembly, Ensembl, FGENESH , GenScan and ...
Genome Research
15:54-66, 2005
Gene and alternative splicing annotation with AIR
Liliana Florea1,4,5 et al
1 Informatics Research, Applied Biosystems, Rockville, Maryland 20850, USA;
... Ab initio prediction programs such as GenScan (Burge and Karlin 1997 ),
FGENESH (Salamov and Solovyev 2000 ), Genie (Kulp et al. ...
Nucleic Acids Research
2005, Vol. 33, Database issue D399-D402
SilkDB: a knowledgebase for silkworm biology and genomics
Jing Wang1 et al
1 College of Life Sciences, Peking University, Beijing 100871, China,
... BGF is a self-developed ab initio program based on GenScan (9) and FGENESH (10),
and was successfully utilized for our rice genome annotation (11). ...
Clinical Cancer Research
Vol. 11, 4029-4036, June 1, 2005
A Molecular Signature in Superficial Bladder Carcinoma Predicts Clinical Outcome
Lars Dyrskjot1 et al
Authors' Affiliations: 1 Molecular Diagnostic Laboratory, Department of Clinical Biochemistry
... array comprising 59,619 probe sets representing 46,000 unique sequences, including
known genes, expressed sequence tag clusters, and FGENESH-predicted exons ...
BMC Evolutionary Biology
2005, 5:1
The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants
Yuanji Zhang* and Liangjiang Wang
Address: Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73402, USA
... Despite minor differences in the gene structure prediction, both gene prediction programs FGENESH and GENSCAN agree on the major features of the protein ...
PLoS Biol.
2005 June; 3(6): e181.
RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons
Vladimir V Kapitonov1 and Jerzy Jurka1
1Genetic Information Research Institute, Mountain View, California, United States of America
David Nemazee, Academic Editor
... Using FGENESH [33], we detected that the RAG1 core-like open reading frame (ORF)
in the contig 29068 forms a terminal exon (positions 1154-2947) of an ...
Genetics
Published Articles Ahead of Print, published on February 16, 2005 as 0.1534/genetics.104.036327
Identification and Characterization of Regions of the Rice Genome Associated with Broad-
Spectrum, Quantitative Disease Resistance
Randall J. Wisser R.J * et al.
*Department of Plant Breeding and Genetics, Institute for Genomic Diversity, Cornell
University, Ithaca, New York 14853
... GENSCAN (B URGE and K ARLIN 1997) and FGENESH (S ALAMOV and S OLOVYEV 2001)
to predict open reading frames. Further searches against ...
Plant Physiology
January 2005, Vol. 137, pp. 176-189
Annotations and Functional Analyses of the Rice WRKY Gene Superfamily Reveal Positive and Negative Regulators of Abscisic Acid Signaling in Aleurone Cells1,[w]
Zhen Xie2 et al
Department of Biological Sciences, University of Nevada, Las Vegas, Nevada 89154
... First of all, three genes (OsWRKY41, -43, and -44) were reannotated using FGENESH
(www.softberry.com), because the first introns of these genes were too small ...
PLoS Biol
3(6): e181 (2005)
RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons.
Vladimir V. Kapitonov1*, Jerzy Jurka1*
1 Genetic Information Research Institute, Mountain View, California, United States of America
... Using FGENESH [33], we detected that the RAG1 core-like open reading frame (ORF)
in the contig 29068 forms a terminal exon (positions 1154-2947) of an ...
Plant and Cell Physiology 2005 46(1):3-13; doi:10.1093/pcp/pci503
From Mapping to Sequencing, Post-sequencing and Beyond
Takuji Sasaki1, Takashi Matsumoto, Baltazar A. Antonio and Yoshiaki Nagamura
National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
... The gene predictions by programs such as Genescan (Burge and Karlin 1997 ), FGENESH
[see Appendix 1 (4)] and Genemark [see Appendix 1 (5)], BLAST (Altschul et ...
Nature Biotechnology, 2005
Improving the nutritional value of Golden Rice through increased pro-vitamin A content
JA Paine, CA Shipton, S Chaggar, RM Howells, MJ ...
... Arabidopsis thaliana psy and rice psy (AY024351) genes identified genomic sequences
of similarity in which genes were predicted using FGENESH algorithm with ...
Genetics
Published Articles Ahead of Print, published on January 16, 2005 as 10.1534/genetics.104.035543
THE GENETIC BASIS FOR INFLORESCENCE VARIATION BETWEEN FOXTAIL AND GREEN MILLET (POACEAE)
Andrew N. Doust*, Katrien M. Devos1, Mike D. Gadberry*, Mike D. Gale, & Elizabeth A. Kellogg*
*University of Missouri-St. Louis, Department of Biology, One University Boulevard, St.
Louis, MO 63121, USA
... Each of these contigs was scanned using FGENESH (S ALAMOV and S OLOVYEV
2000), and open reading frames (ORFs) were translated and ...
PLoS Biol
3(1): e13 January 2005
Sorghum Genome Sequencing by Methylation Filtration
Joseph A. Bedell et al.
Bioinformatics, Orion Genomics, Saint Louis, Missouri, United States of America,
... additional parameters: wordmask=seg; lcmask; M=1; N=-1; Q=3; R=3; kap; E=1e-10;
hspmax=0. To look for potentially novel genes, we used FGENESH (http://www ...
BMC Genomics
2005, 6:11 doi:10.1186/1471-2164-6-11
FAM20: an evolutionarily conserved family of secreted proteins expressed in hematopoietic cells
Demet Nalbant et al.
Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, USA
... These results were compared against genes assembled by two gene prediction programs,
FGENESH: http://www.softberry.com/berry.phtml and GENSCAN: http://genes.mit ...
Plant Physiology
July 2005, Vol. 138, pp. 1205-1215
Complex Organization and Evolution of the Tomato Pericentromeric Region at the FER Gene Locus1,[w]
Romain Guyot et al.
Institute of Plant Biology, University of Zurich, 8008 Zurich, Switzerland (R.G., E.S., B.K., H.-Q.L.); and Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China (X.C., Y.S., Z.C., H.-Q.L.)
... Putative genes were determined by a combination of coding region prediction software
(GENSCAN, FGENESH, and MZEF with Arabidopsis and/or monocot matrix ...
J Gen Virol
86 (2005), 973-983; DOI 10.1099/vir.0.80833-0
Cloning, characterization and analysis by RNA interference of various genes of the Chelonus inanitus polydnavirus
Marianne Bonvin et al
Institute of Cell Biology, University of Berne, Baltzerstrasse 4, CH-3012 Bern, Switzerland
... 12g1forw (5'-GAGTCCATGCCGAATGTCAC-3') and 12g1rev (5'-CTTCTTGCACAGCGACGAAC-3') were set to amplify the middle region of 12g1, as predicted with FGENESH 1.0 and ...
BMC Plant Biol.
2005, 5:15
Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana
Mudge et al.,
1Dept of Plant Pathology, 495 Borlaug Hall, University of Minnesota, St. Paul, MN 55108 USA
... Genes were predicted in G. max and M. truncatula genomic sequences using the dicot
(Arabidopsis) matrix of FGENESH [59,60]http://www.softberry.com webcite. ...
PNAS
February 1, 2005 vol. 102 no. 5 1566-1571
A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome
Mark Yandell et al
Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Life Sciences Addition, Berkeley, CA 94720-3200; and Department of Genome Sciences, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop 64-121, Berkeley, CA 94720
... genes, based on a microarray-based approach that involved hybridizing randomly primed
cDNA against probes corresponding to a large set of FGENESH predictions. ...
Insect Molecular Biology
Volume 14 Issue 2 Page 113 - 119 April 2005
Detection and analysis of alternative splicing in the silkworm by aligning expressed sequence tags with the genomic sequence
X.-F. Zha et al
Correspondence: Dr Qing-You Xia, The Key Sericultural Laboratory of Agricultural Ministry, Southwest Agricultural University, Chongqing 400716, China.
... previously predicted silkworm genes in the genomic sequences by BGF, a newly developed
program based on GENSCAN (Burge & Karlin, 1997) and FGENESH (Salamov & ...
Microbiology
151 (2005), 2199-2207;
DOI 10.1099/mic.0.27962-0
Overproduction, purification and characterization of FtmPT1, a brevianamide F prenyltransferase from Aspergillus fumigatus
Alexander Grundmann and Shu-Ming Li
Pharmazeutische Biologie, Pharmazeutisches Institut, Eberhard-Karls-Universitat Tubingen, Auf der Morgenstelle 8, 72076 Tubingen, Germany
... FGENESH (Softberry, Inc., http://www.softberry.com/berry.phtml) and the DNASIS software
package (version 2.1; Hitachi Software Engineering) were used for ...
Fungal Genetics and Biology
Volume 41, Issue 1, January 2004, Pages 23-32
Contig assembly and microsynteny analysis using a bacterial artificial chromosome library for Epichloe festucae, a mutualistic fungal endophyte of grasses
Brandi L Kutil a, Gang Liu a, 1, Julia Vrebalov b and Heather H Wilkinson
aDepartment of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77845-2132, USA
bBoyce Thompson Institute for Plant Research, Ithaca, NY 14853-1801, USA
... Contigs were also submitted to FGENESH (http://www.softberry.com/berry.phtml)
to predict ORFs using N. crassa as the training set. ...
Eukaryotic Cell
April 2004, p. 420-429, Vol. 3, No. 2
Cryptococcus neoformans Virulence Gene Discovery through Insertional Mutagenesis
Alexander Idnurm, Jennifer L. Reedy, Jesse C. Nussbaum, and Joseph Heitman
Department of Molecular Genetics and Microbiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina 27710
... FGENESH software (SoftBerry) was used to search for coding regions within the sequence,
and BLAST searches were conducted against the GenBank database to infer ...
Breeding Science
Vol. 54 (2004) , No. 2 165-175
Molecular Characterization of a 313-kb Genomic Region Containing the Self-incompatibility Locus of Ipomoea trifida, a Diploid Relative of Sweet Potato
Rubens Norio Tomita et al.,
1) Faculty of Bioresources, Mie University
2) Division of Natural Science, Osaka Kyoiku University
3) Life Science Research Center, Mie University
... gatech.edu/GeneMark), GENE- SCAN (http://genes.mit.edu/GENESCAN), GlimmerM (http://
www.tigr.org/tdb.glimmerm/glmr) and FGENESH (http:// softberry.com/berry ...
J. Biol. Chem
Vol. 279, Issue 18, 18550-18558, April 30, 2004
The Two-pore Domain K+ Channel, TRESK, Is Activated by the Cytoplasmic Calcium Signal through Calcineurin
Gabor Czirjak, Zsuzsanna E. Toth, and Peter Enyedi
From the Department of Physiology and Laboratory of Neuromorphology, Semmelweis University, H-1444 Budapest, Hungary
... The conceptual coding region of the new channel was calculated from the neighboring
genomic sequences by the FGENESH program at the Softberry site on the World ...
Genome Res.
2004. 14: 1916-1923 doi:
10.1101/gr.2332504
Close Split of Sorghum and Maize Genome Progenitors
Swigonova et al.,
1Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854, USA
2Department of Biological Sciences and Genetics Program, West Lafayette, Indiana 47907, USA
... Genes predicted by FGENESH (www.softberry.com) and GENSCAN (http://genes.mit.edu/
GENSCAN.html) programs were further analyzed by homology searches using BLAST ...
PNAS
October 26, 2004 vol. 101 no. 43 15289-15294
Estimating genome conservation between crop and model legume species
Choi et al.,
Department of Plant Pathology and §College of Agricultural and Environmental Sciences Genomics Facility, University of California, One Shields Avenue, Davis, CA 95616; ¶Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
... NCBI (18). Ab initio gene prediction involved the eudicot version of fgenesh
(www.softberry.com/berry.phtml?topic=gfind). Gene prediction ...
PNAS
January 20, 2004 vol. 101 no. 3 700-707
Pattern of diversity in the genomic region near the maize domestication gene tb1
Richard M. Clark†, Eric Linton‡,§, Joachim Messing‡, and John F. Doebley†
†Laboratory of Genetics, University of Wisconsin, Madison, WI 53706; and ‡Waksman Institute, Rutgers University, Piscataway, NJ 08854
... default" and DNA source set to "Grasses." Nonrepetitive DNA was analyzed for genes
by using the fgenesh gene prediction software (www.softberry.com/berry ...
Eukaryotic Cell
October 2004, p. 1088-1100, Vol. 3, No. 5
Introns and Splicing Elements of Five Diverse Fungi
Kupfer et al.,
Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City,2 Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma,1
... Translation of the DNA sequences was done by using FGENSH at the Softberry website
(http://www.softberry.com/) with either the S. pombe or the N. crassa matrix ...
Journal of Experimental Biology
207, 4573-4586 (2004)
Functional characterisation of the Anopheles leucokinins and their cognate G-protein coupled receptor
Jonathan C. Radford, Selim Terhzaz, Pablo Cabrero, Shireen-A. Davies and Julian A. T. Dow
Institute of Biomedical and Life Sciences, Division of Molecular Genetics, University of Glasgow, Glasgow G11 6NU, UK
... This region plus the surrounding 20 kb of genomic sequence either side was then
analysed with the Softberry FgenesH gene prediction program (www.softberry.com ...
TAG Theoretical and Applied Genetics
Issue: Volume 109, Number 4 Date: August 2004 Pages: 681 - 689
Linkage disequilibrium and sequence diversity in a 500-kbp region around the adh1 locus in elite maize germplasm
Mark Jung et al
(1) DuPont Crop Genetics, Experimental Station, P.O. Box 80353, Wilmington, DE 19880-0353, USA
... 1). Gene locations were defined by several methods. Annotations provided in Tikhonov
et al. (1999) were first used, then FGENESH gene-finding software ...
DNA Sequence - The Journal of Sequencing and Mapping
Issue: Volume 15, Number 4 / August, 2004 Pages: 269 - 276
Isolation, Characterization and Expression Analysis of a Leaf-specific Phosphoenolpyruvate Carboxylase Gene in Oryza sativa
Chang-Fa Lin et al
State Key Laboratory of Genetic Engineering Institute of Genetics, School of Life Sciences, Fudan University Shanghai 200433 P.R.China
... tools of GeneMark (http://opal. biology.gatech.edu/geneMark/) and Softberry
(http://www.softberry.com). For the isolation of putative ...
Nature Genetics
36, 40 - 45 (01 Jan 2004)
Complete sequencing and characterization of 21,243 full-length human cDNAs
Ota et al.
...PSORT II, http://psort.ims.u-tokyo.ac.jp/; DIGIT, http://digit.ims.u-tokyo.ac.jp;
FGENESH, http://www.softberry.com/berry.phtml; GENSCAN, http://genes.mit.edu/GENSCAN.html; HMMGENES, http://www.cbs.dtu.dk/services/HMMgene/; HUNT...
Plant Molecular Biology
Issue: Volume 54, Number 4 Date: March 2004 Pages: 519 - 532
Genome-Wide Analysis of the GRAS Gene Family in Rice and Arabidopsis
Chaoguang Tian1, Ping Wan1, Shouhong Sun1, Jiayang Li1 and Mingsheng Chen1*
(1) Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China
... database. FGENESH (Salamov and 90 Solovyev, 2000) was used for gene prediction. ...
pre- 207 dicted by FGENESH (minor discrepancies exist due 208 ...
Mycological Research
(2004), 108: 853-857 Cambridge University Press
Combining transcriptome data with genomic and cDNA sequence alignments to make confident functional assignments for Aspergillus nidulans genes
Andrew H. SIMS a1, Manda E. GENT a1, Geoffrey D. ROBSON a1, Nigel S. DUNN-COLEMAN a2 and Stephen G. OLIVER a1c1
a1 School of Biological Sciences, University of Manchester, The Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.
... Kingdom. Page 2. Genewise, FGENESH, FGENESH+) consisting of 9541 putative
open reading frames (ORFs) was released in June 2003. We ...
TAG Theoretical and Applied Genetics
Issue: Volume 109, Number 1 Date: June 2004 Pages: 129 - 139
Gene content and density in banana (Musa acuminata) as revealed by genomic sequencing of BAC clones
R. Aert1, 2, L. Sagi2 and G. Volckaert1
(1) Laboratory of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
Present address: Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, (2) Kasteelpark Arenberg 13, 3001 Leuven, Belgium
... gsc.riken.go.jp), FGENESH version 1.1 (Salamov and Solovyev 2000; http://www.softberry.
com), genemark.hmm version 2.2a (Lukashin and Borodovsky 1998; http ...
Genome Research
14:2503-2509, 2004
EAnnot: A genome annotation tool using experimental evidence
Li Ding et al
Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri 63110, USA
...Some ab initio programs, such as Genscan (Burge and Karlin 1997 ) and FGENESH (Salamov and Solovyev 2000 ) are based on intrinsic characteristics of coding sequence (e.g., codon usage, consensus splice sites, etc.) and require training on known genes from the organism...
TAG Theoretical and Applied Genetics
Issue: Volume 109, Number 7 Date: November 2004 Pages: 1434 - 1447
Full-genome analysis of resistance gene homologues in rice
B. Monosi1, R. J. Wisser2, L. Pennill1 and S. H. Hulbert1
(1) Department of Plant Pathology, Kansas State University, Manhattan, KS 66506-5502, USA
(2) Department of Plant Pathology, Cornell University, Ithaca, NY 14853, USA
... DNA sequences were analyzed using the gene prediction programs GENSCAN (Burge and
Karlin 1997; http://genes.mit.edu/GENSCAN.html) and FGENESH (Salamov and ...
arXiv:q-bio.GN/0402046 v1 27 Feb 2004
Sublinear growth of Information in DNA sequences
Giulia Menconi
Dipartimento di Matematica Applicata and C.I.S.S.C. Centro Interdisciplinare
per lo Studio dei Sistemi Complessi Universit`a di Pisa
Via Bonanno Pisano 25/b 56126 PISA - Italy
...As a result, four putative genes G1, G2, G3 and G4 have been located by means of Hidden Markov Model-based program FGENESH2 that has been created for predicting multiple genes and their structure in genomic DNA sequences. The analysis via FGENESH has been exploited with respect to known genes in Arabidopsis thaliana. Their predicted position is illustrated in Figure 13.
...2This program is available at the website www.softberry.com to which we refer con-cerning the reliability and e_ciency of the algorithm....
Current Opinion in Plant Biology
2004, 7:732-736
Consistent over-estimation of gene number in complex plant genomes
Jeffrey L Bennetzen1,4, Craig Coleman2,7, Renyi Liu1,5, Jianxin Ma1,6 and
Wusirika Ramakrishna3,8
1 Department of Genetics, University of Georgia, Athens, Georgia 30602,
USA
...We have found that the standard gene-discovery programs FGENESH, GeneMark and GENSCAN annotate segments of most retrotransposons and many invertedrepeat transposable elements as genes. Using FGENESH to annotate maize BAC clones, for instance, 70-100% of the predicted genes are actually from transposable elements...
The Plant Cell
16:2795-2808 (2004)
Spotted leaf11, a Negative Regulator of Plant Cell Death and Defense, Encodes a U-Box/Armadillo Repeat Protein Endowed with E3 Ubiquitin Ligase Activity
Li-Rong Zeng et al
a Department of Plant Pathology, Ohio State University, Columbus, Ohio 43210
... in spl11. Exons predicted in G3 by the programs GENSCAN and FGENESH using
different matrixes are displayed in dark gray. (D) RFLP ...
Human Genomics,
Volume 1, Number 2, January 2004, pp. 146-149(4)
The truth about mouse, human, worms and yeast
Authors: David R. Nelson1; Daniel W. Nebert2
1: Department of Molecular Sciences and The UT Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, Tennessee 38163, USA 2: Department of Environmental Health and Center for Environmental Genetics (CEG), University of Cincinnati Medical Center, Cincinnati, Ohio 45267-0056, USA
... unpublished data, 2003; see also Ref. [7]), FGENESH, 21 TWINSCAN 22 and
the Ensembl annotation pipeline. 23 The output of the four ...
Genome Biology
2004, 5:R73 doi:10.1186/gb-2004-5-10-r73
A comprehensive transcript index of the human genome generated using microarrays and computational approaches
Eric E Schadt et al
1Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
...GrailEXP 4.0 [47], GENSCAN 1.0 [48], FGENESH [49], and FGENESH+ [49]ab initio gene-prediction algorithms were run independently across the entire genome assembly to augment alignment-based gene identification methods...
Genome Research
14:988-995, 2004
GeneWise and Genomewise
Ewan Birney1,3, Michele Clamp2 and Richard Durbin2
1 The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; 2 The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
...There has been a long history of successful ab initio programs which do not use any additional evidence to predict genes on genomic DNA, of which Genscan (Burge and Karlin 1997 ) and FGENESH (Solovyev and Salamov 1997 ) are two of the most successful cases....
...Another class of evidence-based gene prediction programs are ones which use external evidence to influence the scoring of potential exons, including SGP-2 (Parra et al. 2003 ), Genie (Kulp et al. 1996 ), Genomescan (Yeh et al. 2001 ), HMMGene (Krogh 2000 ), and FGENESH++ (Solovyev and Salamov 1997 )...
PNAS
February 17, 2004 vol. 101 no. 7 1910-1915
Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms
Jongmin Nam et al
Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802
...Because annotation of rice gene was still in progress at the
time of this study, we ourselves conducted gene annotation by using the
computer program FGENESH (www.softberry.com) from the genome sequences obtained from TIGR and the Rice Genome Database (China) (25).
Functional & Integrative Genomics
Issue: Volume 4, Number 2 Date: May 2004 Pages: 102 - 117
Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny
Nagendra K. Singh et al.,
Indian Initiative for Rice Genome Sequencing, National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
... Wherever RiceGAAS data were not available, the genes were predicted by FGENESH trained
for monocot plant species (http:// www.softberry.com/berry.phtml). ...
TAG Theoretical and Applied Genetics
Issue: Volume 109, Number 1 Date: June 2004 Pages: 10 - 22
Annotation of a 95-kb Populus deltoides genomic sequence reveals a disease resistance gene cluster and novel class I and class II transposable elements
M. Lescot et al
1. Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, 9052 Gent, Belgium
... 1999; http://www.tigr.org/tdb/glimmerm/glmr_form.html), and FGENESH for dicots or
monocots (Salamov and Solovyev 2000; http://www.softberry.com/). ...
BIOINFORMATICS,
2004 vol.20 N.9 p.1416-1427
J Yuan, B Bush, A Elbrecht, Y Liu, T Zhang, W Zhao ... -
... suchasGRAIL(Lopezetal., 1994; Roberts, 1991; Uberbacher et al., 1996), GENESCOPE
(Murakami and Takagi, 1998), FGENESH (Salamov and Solovyev, 2000), GeneMark ...
Molecular Plant Pathology
Volume 5 Issue 6 Page 515 - November 2004
Heading for disaster: Fusarium graminearum on cereal crops
RUBELLA S. GOSWAMI AND H. CORBY KISTLER
... This pipeline uses a combination of the programs FGENESH and FGENESH+ (Salamov and Solovyev, 2000) modified by Softberry ( http:/ / www.softberry.com ) with ...
Nucleic Acids Research
2004, Vol. 32, Database issue D41-D44
MIPS: analysis and annotation of proteins from whole genomes
H. W. Mewes et al
1 Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany and 2 Technische Universitat Munchen, Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, D-85350 Freising-Weihenstephan, Germany
... The genome of 40 Mb encodes 10 000 proteins automatically predicted by the program FGENESH (http://softberry. com), specifically trained for Neurospora. ...
Annual Review of Genomics and Human Genetics
Vol. 5: 15-56 (Volume publication date September 2004)
COMPARATIVE GENOMICS
Webb Miller, Kateryna D. Makova, Anton Nekrutenko, and Ross C. Hardison
The Center for Comparative Genomics and Bioinformatics, The Huck Institutes of Life Sciences, and the Departments of Biology, Computer Science and Engineering, and Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania
... These algorithms include Genscan, the most popular gene prediction tool (24), GenMark
(117), FGENESH (155), GeneID (144), and others (for an excellent overview ...
DNA and Cell Biology
May 2004, Vol. 23, No. 5: 311-324
Harbinger Transposons and an Ancient HARBI1 Gene Derived from a Transposase
Vladimir V. Kapitonov , Jerzy Jurka
Genetic Information Research Institute, Mountain View, California.
... We used FGENESH (Salamov and Solovyev, 2000) and GeneScan (Burge and Karlin, 1997)
for the identification of exons and introns. The d N /d S ratio, ...
Nucleic Acids Research
2004, Vol. 32, Database issue D377-D382
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics
Wenming Zhao et al
1 Beijing Genomics Institute (BGI), Chinese Academy of Sciences (CAS), Beijing Airport Industrial Zone-B6, Beijing 101300, China
... The contig sequences were annotated for gene content by using automated processes
that involve ab initio gene finders, such as FGENESH (http://www.softberry.com ...
Genome Research
14:1932-1937, 2004
Characterization of the Maize Endosperm Transcriptome and Its Comparison to the Rice Genome
Jinsheng Lai et al
1 Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA;
... A total of 54,397 putative genes could be predicted for the rice genome from this
data set (Table 3) using the FGENESH program with the default setting for ...
Plant Molecular Biology
Issue: Volume 54, Number 1 Date: January 2004 Pages: 55 - 69
Dynamics of the evolution of orthologous and paralogous portions of a complex locus region in two genomes of allopolyploid wheat
Xiu-Ying Kong1, 2, Yong Qiang Gu3, Frank M. You4, Jorge Dubcovsky4 and Olin D. Anderson3
1. Genetic Resources Conservation Program, University of California, Davis, CA 95616, USA
2. Institute of Crop Germplasm Resources, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
3. U.S. Dept. of Agriculture, Western Regional Research Center, Agricultural Research Service, 800 Buchanan Street, Albany, CA 94710, USA
4. Department of Agronomy and Range Sciences, University of California, Davis, CA 95616, USA
... FGENESH (http://www.softberry.com/berry.phtml) and GENES- CAN (http://genemark.
mit.edu/GENESCAN.html) were used for gene prediction. ...
Current Genetics
Issue: Volume 44, Number 6 Date: January 2004 Pages: 329 - 338
Chromosome rearrangements in isolates that escape from het-c heterokaryon incompatibility in Neurospora crassa
Qijun Xiang1 and N. Louise Glass1
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
... Hypothetical proteins are predicted from FGENESH calls with overlapping Blastx
hits (but not with trusted homology), while Predicted ...
Molecular Genetics and Genomics
Issue: Volume 271, Number 4 Date: May 2004 Pages: 402 - 415
Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes
T. Zhou et al
1. State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, 210093 Nanjing, China
... to 5000-10,000 bp from both ends of the hits, and then the expanded nucleotide
fragments were reannotated using the gene-finding programs FGENESH (http:// www ...
Proc Natl Acad Sci U S A.
2004 June 15; 101(24): 9045-9050.
Genetic control of branching in foxtail millet
Andrew N. Doust et al
*Department of Biology, University of Missouri, 8001 Natural Bridge Road, St Louis, MO 63121; and ‡John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom
... Each of these contigs was scanned by using FGENESH (28), and identified ORFs were translated and compared with ORFs from other contigs from the same QTL region ...
Mol. Biol. Evol.
21(9):1769-1780. 2004
Merlin, a New Superfamily of DNA Transposons Identified in Diverse Animal Genomes and Related to Bacterial IS1016 Insertion Sequences
Cedric Feschotte1
Departments of Plant Biology and Genetics, The University of Georgia, Athens
... coding sequences were assembled by removing introns predicted with more than 85%
confidence by NetGene2 (http://www.cbs.dtu.dk) and/or FGENESH (http://genomic ...
Genome Research
14:1924-1931 ©2004
Gene Loss and Movement in the Maize Genome
Jinsheng Lai et al
1Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020, USA; 2Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA
... The FGENESH program predicted four, of which three (gene 1d in the maize orp1 region; gene 5a, 5b in the rice r1 region) would produce truncated proteins ...
Internal Medicine Journal
Volume 34 Issue 3 Page 79 -90 - March 2004
Systematic genome-wide approach to positional candidate cloning for identification of novel human disease genes
H. Kiyosawa et al
Affiliations: 1Technology and Development team for Mammalian Cellular Dynamics, Bioresource Center, RIKEN Tsukuba Institute, Tsukuba, Ibaraki
...Page 1. Internal Medicine Journal 2004; 34: 79-90. O RIGINAL A RTICLE. Systematic
genome-wide approach to positional candidate. cloning ...
Molecular Microbiology
Volume 54 Issue 2 Page 407 - October 2004
Cryptococcus neoformans Kin1 protein kinase homologue, identified through a Caenorhabditis elegans screen, promotes virulence in mammals
Eleftherios Mylonakis et al
1Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA.
... Sequences were compared with the H99 genome database at Duke University, and genes
predicted in these regions by FGENESH software ( http:/ / www.softberry.com ...
TAG Theoretical and Applied Genetics
Issue: Volume 108, Number 5 Date: March 2004 Pages: 903 - 913
Characterization of soybean genomic features by analysis of its expressed sequence tags
Ai-Guo Tian et al
1. Plant Biotechnology Laboratory, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, 100101 Beijing, China
... six BAC-contig sequences of M. truncatula were analyzed and the results based on the gene prediction program FGENSH (Arabidopsis match/FGENESH prediction) (http ...
Current Proteomics,
Volume 1, Number 1, January 2004, pp. 41-48(8)
Annotation of the Human Genome by High-Throughput Sequence Analysis of Naturally Occurring Proteins
McGowan S.J.1; Terrett J.1; Brown C.G.1; Adam P.J.1; Aldridge L.1; Allen J.C.1; Amess B.1; Andrews K.A.1; Barnes M.1; Barnwell D.E.1
1: Oxford GlycoSciences plc, The Forum, 86 Milton Park, Abingdon, OX14 4RY, UK
... The polymorphic 'hypothetical transcriptome' was cons- tructed from transcripts
predicted by FGENES, FGENESH (Softberry Inc, Mount Kisco, NY, USA), GENSCAN ...
Chinese Science Bulletin
2004 Vol. 49 No. 4 355-362
The VER2 promoter contains repeated sequences and requires vernalization for its activity in winter wheat (Triticum aestivum L.)
XU Wenzhong et al
1. Research Center for Molecular Developmental Biology, Key Lab of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences (CAS), Beijing 100093, China;
... Sequence analyses were finished using biological softwares on Internet, such as FGENESH 1.0 (Prediction of potential genes in Plant (Dct) genomic DNA). ...
TAG Theoretical and Applied Genetics
Issue: Volume 108, Number 3 Date: February 2004 Pages: 392 - 400
Sequence variations of simple sequence repeats on chromosome-4 in two subspecies of the Asian cultivated rice
Can Li1, Yu Zhang1, Kai Ying1, Xiaolei Liang1 and Bin Han1
(1) National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
... To characterize the possible relationship between SSRs and genes predicted by using
FGENESH, we investigated the distribution of SSRs in the rice chromosome-4 ...
Proc Natl Acad Sci U S A.
2004 June 29; 101(26): 9885-9890.
Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep
Kelly Palaisa,* Michele Morgante, Scott Tingey, and Antoni Rafalski*
DuPont Crop Genetics, Molecular Genetics Group, 1 Innovation Way, Newark, DE 19711; *Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716
... The Y1 gene comprises a small uninterrupted gene island consisting of the Y1, an
MLO homolog lying immediately downstream of Y1, and an FGENESH-predicted gene ...
TAG Theoretical and Applied Genetics
Issue: Volume 108, Number 8 Date: May 2004 Pages: 1449 - 1457
Positional cloning of the rice Rf-1 gene, a restorer of BT-type cytoplasmic male sterility that encodes a mitochondria-targeting PPR protein
H. Akagi et al
1. Laboratory of Plant Breeding and Genetics, Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Kaidoubata-Nishi 241-7, Shimoshinjyo-Nakano, 010-0195 Akita, Japan
... Software Develop- ment, Tokyo). Genomic sequences were also analyzed using
gene prediction programs, genescan and FGENESH. Table 1 DNA ...
Genome Research
14:942-950, 2004
The Ensembl Automatic Gene Annotation System
Val Curwen et al
1 The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; 2 EMBL European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK; 3 The Broad Institute, Cambridge, Massachusetts 02141, USA
... Commonly, we use Genscan for ab initio prediction in human, mouse, and rat, but
the system is equally applicable to other methods such as FGENESH (Solovyev et ...
Gene
324 (2004) 105-115
Transcript abundance of rml1, encoding a putative GT1-like factor in rice, is up-regulated by Magnaporthe grisea and down-regulated by light
Rong Wang a,b, Guofan Honga,b, Bin Hana,*
National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
... 1A and 2A). The structure of rml1 _ a is as same as that predicted by FGENESH software.
The 3V UTR of rml1 _ a is confirmed with the length of 596 bp. ...
Genome Biology
2004, 5:R46 doi:10.1186/gb-2004-5-7-r46
Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. Indica
Cizhong Jiang1, Xun Gu1, 2 and Thomas Peterson1
1Department of Genetics, Development and Cell Biology, and Department of Agronomy, Iowa State University, Ames, IA 50011, USA
2LHB Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA
... FGENESH has been used successfully to predict genes in rice [9], and GenScan was
used together with it to predict genes by taking rice genomic sequences as ...
Molecular Microbiology
53 (5), 1307-1318. - September 2004
The sirodesmin biosynthetic gene cluster of the plant pathogenic fungus Leptosphaeria maculans
Donald M. Gardiner et al
1School of Botany, The University of Melbourne, Victoria, Australia 3010.
... http:/ / www.tigr.org . Putative genes were predicted using FGENESH software
at http:/ / www.softberry.com. Fungal culture. The wild type ...
Journal of Molecular Evolution
Issue: Volume 59, Number 6 Date: December 2004 Pages: 761 - 770
Analysis of the Molecular Evolutionary History of the Ascorbate Peroxidase Gene Family: Inferences from the Rice Genome
Felipe Karam Teixeira1, Larissa Menezes-Benavente1, Rogerio Margis1, 2 and Marcia Margis-Pinheiro1
(1) Laboratorio de Genetica Molecular Vegetal, Departamento de Genetica, UFRJ, 21944-970 Rio de Janeiro, Brasil
(2) Departamento de Bioquimica, Instituto de Quimica, UFRJ, 21944-970 Rio de Janeiro, Brasil
... Genomic se- quences were also analyzed in the FGENESH gene structure pre- diction
program (http://www.softberry.com/) (Solovyev 2001) and GeneMark program (http ...
Journal of Biotechnology
109 (2004) 217-226
Preparation of single rice chromosome for construction of a DNA library using a laser microbeam trap
Xiaohui Liu et al
A National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
... ers. These sequences were further annotated using gene-prediction software
FGENESH to give the pos- sible protein-coding region. ...
Science
2004, 303: 1364-1367.
Medicago truncatula DMI1 Required for Bacterial and Fungal Symbioses in Legumes
Ane et al. (2004).
... 17. HK Choi et al., Genetics, in press. 18. FGENESH, see www.softberry.com/berry.
phtml. 19. E. Bornberg-Bauer, E. Rivals, M. Vingron, Nucleic Acids Res. ...
Proc Natl Acad Sci U S A.
2004 August 24; 101(34): 12404-12410.
Inaugural Articles
Rapid recent growth and divergence of rice nuclear genomes
Jianxin Ma and Jeffrey L. Bennetzen*
Department of Genetics, University of Georgia, Athens, GA 30602
... Almost all LTR-retrotransposons, including solo LTRs, identified in our studies
were predicted as genes by the gene-finding program FGENESH (data not shown). ...
The Plant Journal
Volume 37 Issue 4 Page 517 -527 - February 2004
Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein
Xinli Sun, Yinglong Cao, Zhifen Yang, Caiguo Xu, Xianghua Li, Shiping Wang* and Qifa Zhang
National Key Laboratory of Crop Genetic Improvement, National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan 430070, China
... al., 1997). Gene prediction programs used were genscan (Burge and Karlin,
1997) and FGENESH (http://www.softberry.com). Promoter ...
TAG Theoretical and Applied Genetics
Issue: Volume 109, Number 3 Date: August 2004 Pages: 515 - 522
Physical mapping and putative candidate gene identification of a quantitative trait locus Ctb1 for cold tolerance at the booting stage of rice
K. Saito1 , Y. Hayano-Saito1, W. Maruyama-Funatsuki1, Y. Sato1 and A. Kato1
(1) National Agricultural Research Center for Hokkaido Region, Hitsujigaoka 1 , Toyohira, Sapporo, Hokkaido, 062-8555, Japan
... GENSCAN , RICEHMM , FGENESH , MZEF ), a splice prediction program ( SPLICEPREDIC-
TOR ), homology search analysis programs ( BLAST , HMMER , ...
TAG Theoretical and Applied Genetics
Issue: Volume 109, Number 4 Date: August 2004 Pages: 690 - 699
The anthracnose resistance locus Co-4 of common bean is located on chromosome 3 and contains putative disease resistance-related genes
M. Melotto1, 4 , M. F. Coelho1, A. Pedrosa-Harand2, J. D. Kelly3 and L. E. A. Camargo1
1. Departamento de Fitopatologia, Laboratorio de Genetica Molecular, ESALQ, Universidade de Sao Paulo, Piracicaba, SP, C.P. 9, 13418-900, Brazil
... and Karlin 1997; http://genes.mit.edu/GENSCAN.html) and FGENESH (http://www.
softberry.com/)-using Arabidopsis as the model or- ganism. ...
Journal of Genetics,
Vol. 83, No. 1, P. 79-99, April 2004
Structural and functional analysis of rice genome
Tyagi A. K. et al
Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road,
New Delhi 110 021, India
... It inte- grates results from several gene prediction software such as GENSCAN (Burge
and Karlin 1997), FGENESH (Sala- mov and Solovyev 2000), RiceHMM (Sakata ...
The Plant Cell
16:1220-1234 (2004)
Comparative Analysis of the Receptor-Like Kinase Family in Arabidopsis and Rice
Shin-Han Shiua, et al
a Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637
... a permissive E value cutoff of 1. The rice genes from the indica subspecies was
predicted using the whole genome shotgun assembly with FGENESH (Solovyev, 2002 ...
Genome Research
14:1474-1482 (2004) © by Cold Spring Harbor Laboratory Press ISSN 1088-9051/04;
Incongruent Patterns of Local and Global Genome Size Evolution in Cotton
Corrinne E. Grover,1 HyeRan Kim,2 Rod A. Wing,2 Andrew H. Paterson,3 and
Jonathan F. Wendel1,4
1Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA; 2Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721, USA; 3Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
... Potential genes were predicted by three independent programs: FGENESH (http://www.softberry.com/), ...
Plant Physiology,
May 2004, Vol. 135, pp. 459-470
Rapid Genome Evolution Revealed by Comparative Sequence Analysis of Orthologous Regions from Four Triticeae Genomes
Yong Qiang Gu*, Devin Coleman-Derr, Xiuying Kong and Olin D. Anderson
United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, California 94710 (Y.Q.G., D.C.-D., O.D.A.); and Institute of Crop Germplasm Resources, Chinese Academy of Agricultural Sciences, Beijing 100081 China (X.K.)
... FGENESH (http://www.softberry.com/nucleo.html) and GENESCAN (http://genemark.
mit.edu/GENESCAN.htm) were used for gene prediction. ...
Plant Physiology,
October 2004, Vol. 136, pp. 3177-3190
Comparative Sequence Analysis of the Region Harboring the Hardness Locus in Barley and Its Colinear Region in Rice1
Katherine S. Caldwell2, Peter Langridge and Wayne Powell*
Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (K.S.C., W.P.); and School of Agriculture and Wine (K.S.C., P.L.) and Australian Centre for Plant Functional Genomics (P.L.), University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia
... jp/; Sakata et al., 2002 ), which couples the integration of several programs for
the prediction of open reading frames (GENSCAN, RiceHMM, FGENESH, MZEF) with ...
GENES & DEVELOPMENT
18:687-699, 2004
pyramus and thisbe: FGF genes that pattern the mesoderm of Drosophila embryos
Angelike Stathopoulos1, Bergin Tam1, Matthew Ronshaugen1, Manfred Frasch2 and Michael Levine1
1 Department of Molecular and Cell Biology, Division of Genetics & Development, University of California, Berkeley, California 94720-3204, USA; 2 Brookdale Department of Molecular Cell and Developmental Biology, Mount Sinai School of Medicine, New York, New York 10029, USA
... FGF protein sequences used in alignment and phylogenetic reconstruction were gathered from GenBank or inferred from genomic sequence using GENESCAN (Burge and Karlin 1997) and FGENESH...
Genome Research
14:1888-1901, 2004
Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse
Ann-Marie Mallon et al
1 Medical Research Council Mammalian Genetics Unit, Harwell, Oxfordshire, United Kingdom; 2 Wellcome Trust Sanger Institute, Hinxton Genome Campus, United Kingdom; 3 Medical Research Council Rosalind Franklin Centre for Genomics Research, Hinxton Genome Campus, United Kingdom
... Ab initio gene structures were predicted using FGENESH (Salamov and Solovyev 2000) and GENSCAN...
Current Proteomics,
January 2004, vol. 1, no. 1, pp. 41-48(8)
Annotation of the Human Genome by High-Throughput Sequence Analysis of Naturally Occurring Proteins
Authors: McGowan S.J.1; Terrett J.1; Brown C.G.1; Adam P.J.1; Aldridge L.1; Allen J.C.1; Amess B.1; Andrews K.A.1; Barnes M.1; Barnwell D.E.1
Affiliations: 1: Oxford GlycoSciences plc, The Forum, 86 Milton Park, Abingdon, OX14 4RY, UK.
... The polymorphic 'hypothetical transcriptome' was cons- tructed from
transcripts predicted by FGENES, FGENESH (
Softberry Inc, Mount Kisco, NY, USA), GENSCAN ...
Plant Physiology
, 2004
A Genome-Wide Screen Identifies Genes Required for Centromeric Cohesion
JJ Doyle, J Denarie, F Debelle, JC Prome, BB Amor, ...
... 17. HK Choi et al., Genetics, in press. 18. FGENESH, see www.softberry.com/berry.phtml. 19. E. Bornberg-Bauer, E. Rivals, M. Vingron, Nucleic Acids Res. ...
Proc Natl Acad Sci U S A.
2003 July 22; 100(15): 9055-9060.
Gene expression of a gene family in maize based on noncollinear haplotypes
Rentao Song and Joachim Messing*
Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854-8020
.. The FGENESH program (Softberry, Mount Kisco, NY) was used for gene prediction analysis.
Fungal Genetics and Biology
Volume 39, Issue 1, June 2003, Pages 31-37
Analysis of loss of pathogenicity mutants reveals that repeat-induced point mutations can occur in the Dothideomycete Leptosphaeria maculans
Alexander Idnurm and Barbara J. Howlett
School of Botany, The University of Melbourne, Vic. 3010, Australia
... A 6088 bp sequence was obtained (GenBank AF525231) and an open reading frame of
529 amino acids was predicted with FGENESH software (www.softberry.com) with no ...
The Journal of Experimental Biology
206, 1275-1289 (2003)
doi: 10.1242/jeb.00261
Conservation of ecdysis-triggering hormone signalling in insects
Zitnan et al.,
1 Institute of Zoology, Slovak Academy of Sciences, Dubravska cesta 9, 84206 Bratislava, Slovakia
2 Institute of Medical Chemistry and Biochemistry, School of Medicine, Comenius University, Sasinkova 2, 81108 Bratislava, Slovakia
... The complete genomic sequence of the putative Anopheles eth gene was identified
using the Softberry FGENESH gene prediction program (Salamov and Solovyev, 2000 ...
BMC Genomics.
2003; 4: 22.
Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs
Sreedhar Oduru et al
1Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas. USA
... Two gene prediction programs were used FGENESH http://www.softberry.com/berry.phtml
and GENEMARK http://opal.biology.gatech.edu/GeneMark/eukhmm.cgi?org=H ...
Insect Molecular Biology
Volume 12 Issue 4 Page 319 - August 2003
Expression of an Aedes aegypti cation-chloride cotransporter and its Drosophila homologues
V. Filippov, K. Aimanova and S. S. Gill
Affiliations. Department of Cell Biology and Neuroscience, University of California, Riverside, USA
... significant similarity to the Drosophila genes were used for gene structure prediction
with the FGENESH program available on site http:/ / www.softberry.com . ...
Developmental Biology
256 (2003) 276-289
tcl-2 encodes a novel protein that acts synergistically with Wnt signaling pathways in C. elegans
Xiaojun Zhao,a Hitoshi Sawa,b and Michael A. Hermana,*
a Program in Molecular, Cellular and Developmental Biology, Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
b Laboratory for Cell Fate Decision, RIKEN, Center for Developmental Biology 2-2-3 Minatojima-minamimachi Chuo-ku, Kobe 650-0047, Japan
...CbTCL-2 is conceptually translated from a gene predicted by the FGENSH (Salamov and Solovyev, 2000; http://www.softberry.com) using defaults for C. elegans genomic sequences.
Proc Natl Acad Sci U S A.
2003 May 27; 100(11): 6569-6574.
Molecular paleontology of transposable elements in the Drosophila melanogaster genome
Vladimir V. Kapitonov* and Jerzy Jurka*
Genetic Information Research Institute, 2081 Landings Drive, Mountain View, CA 94043
...We used FGENESH (ref. 18; www.softberry.com) for identifying genes encoded by TEs.
Genetics and Molecular Biology
ISSN 1415-4757 version impresa
Genet. Mol. Biol. v.26 n.4 Sao Paulo dic. 2003
Iron homeostasis related genes in rice
Jeferson GrossI, II; Ricardo Jose SteinII; Arthur Germano Fett-NetoI, II; Janette Palma FettI, II
IUniversidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Porto Alegre, RS, Brazil
...The prediction algorithms were GenScan (Burge and Karlin, 1997; http://genes.mit.edu/GENSCAN.html), GenomeScan (Burge and Karlin, 1997; http://genes.mit.edu/genomescan.html), FGENESH (Salamov and Solovyev, 2000; http://www.softberry.com/berry.phtml?topic= gfind), GeneMark.hmm (Borodovsky and Lukashin, unpublished; http://opal.biology.gatech.edu/GeneMark/eukhmm.cgi) and GrailEXP (Xu and Uberbacher, 1997; http://compbio.ornl.gov/grailexp/)...
BMC Plant Biology
2003, 3:6
Ds tagging of BRANCHED FLORETLESS 1 (BFL1) that mediates the transition from spikelet to floret meristem in rice (Oryza sativa L)
Qian-Hao Zhu1,2, Mohammad Shamsul Hoque1,2, Elizabeth S Dennis1,2 and
Narayana M Upadhyaya*1,2
Address: 1CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia and 2NSW Agricultural Genomics Centre, Wagga Wagga, Australia
... Analyses of 10-kb sequence of the ~30-kb contig 239 from the China Rice Genome database harboring the BFL1 locus by gene prediction programs FGENESH http://www.softberry.com/berry.phtml/ and GENSCAN...
..The ORF was identified by using FGENESH http://www.softberry.com/berry.phtml/ and GENSCAN http://genes.mit.edu/GENSCAN.html.
Australasian Plant Pathology
Volume 32 Number 4 2003 pp. 511-519
Small scale functional genomics of the blackleg fungus, Leptosphaeria maculans: analysis of a 38 kb region
Alexander Idnurm, Janet L. Taylor, M. Soledade C. Pedras and Barbara J. Howlett
... vertebrate and Arabidopsis settings; Burge and Karlin 1997) and FGENESH on Neurospora
crassa and Schizosaccharomyces pombe settings (www.softberry.com), as ...
Barley Genetics Newsletter
Volume 32 Hard-copy edition pages 34 - 37
MAPPING AND SEQUENCING OF THE BARLEY PUTATIVE HYPERSENSITIVE INDUCED REACTION GENES
Nils Rostoks1, David Kudrna1 and Andris Kleinhofs1,2
1 Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164
2 School of Molecular Biosciences, Washington State University, Pullman, WA 99164
The full length coding sequence was reconstructed using a combination of FGENESH gene prediction program (http://www.softberry.com/) and alignment with cDNAs from the other barley HIR groups.
TAG Theoretical and Applied Genetics
Issue: Volume 43, Number 5 Date: August 2003 Pages: 351 - 357
Characterisation of the mating-type locus of the plant pathogenic ascomycete Leptosphaeria maculans
Anton J. Cozijnsen A1 and Barbara J. Howlett A1
A1 School of Botany The University of Melbourne 3010 Victoria Australia
...Genes, introns, exons and transcription initiation sites were predicted by analysis with FGENESH (www.softberry.com) on Neurospora crassa and...
BMC Plant Biol.
2003; 3: 6.
Ds tagging of BRANCHED FLORETLESS 1 (BFL1) that mediates the transition from spikelet to floret meristem in rice (Oryza sativa L)
Qian-Hao Zhu et al
1CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
2NSW Agricultural Genomics Centre, Wagga Wagga, Australia
...Analyses of 10-kb sequence of the ~30-kb contig 239 from the China Rice Genome database harboring the BFL1 locus by gene prediction programs FGENESH http://www.softberry.com/berry.phtml/ and GENSCAN http://genes.mit.edu/GENSCAN.html identified a single-exon gene capable of encoding a protein with the DNA binding domain of the EREBP/AP2 family of plant transcription factors [26,36], 1515 bp downstream from the Ds insertion.
.. The ORF was identified by using FGENESH http://www.softberry.com/berry.phtml/ and GENSCAN http://genes.mit.edu/GENSCAN.html. Alignment of EREBP/AP2 domains was performed using programs of Genetics Computer Group Wisconsin software suit [11].
Genetics,
Vol. 164, 655-664, June 2003, Copyright © 2003
Map-Based Cloning of Leaf Rust Resistance Gene Lr21 From the Large and Polyploid Genome of Bread Wheat
Li Huang et al
a Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506-5502
...In addition, FGENSH 1.1 (http://www.softberry.com) was used for gene prediction (with monocot genomic DNA parameters).
Nucleic Acids Research,
2003, Vol. 31, No. 1 229-233
The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists
Qiaoping Yuan et al
The Institute for Genomic Research, 9712 Medical Center Dr., Rockville, MD 20850, USA
...The rice sequences were processed with multiple ab initio gene finders including FGENESH (http://www.softberry.com),...
... Working models were generated using the FGENESH output and putative identification for the gene was obtained from the most significant database match while models with no significant database match were labeled as hypothetical proteins.
Journal of Experimental Botany
, Vol. 54, No. 389, pp. 1995-1996, August 1, 2003
OsSET1, a novel SET-domain-containing gene from rice
Yun-Kuan Liang et al
PKU-Yale Joint Research Center of Agricultural and Plant Molecular Biology, National Key Laboratory of Protein Engineering and Plant Gene Engineering, College of Life Sciences, Peking University, 5 Yiheyuan Road, Beijing 100871, PR China
... It localizes at chromosome three in rice genome at the contig 1300 (http://www.softberry.com/berry.phtml?topic=gfind&prg=FGENESH; GenBank accession number ...
BMC Genomics
2003, 4:22
Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs
Sreedhar Oduru et al
Address: 1Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas. USA
...Two gene prediction programs were used FGENESH http://www.softberry.com/berry.phtml and GENEMARK http://opal.biology.gatech.edu/GeneMark/eukhmm.cgi?org=H.sapiens
TAG Theoretical and Applied Genetics
Issue: Volume 108, Number 5 Date: March 2004 Pages: 903 - 913
Characterization of soybean genomic features by analysis of its expressed sequence tags
Ai-Guo Tian et al
Plant Biotechnology Laboratory, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, 100101 Beijing, China
Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing, China
... prediction of these BAC-contig sequences was based on the gene-prediction program
FGENSH (Arabidopsis match/FGENESH
Nucleic Acids Research
2002, Vol. 30, No. I
31-34
MIPS: a database for genomes and protein sequences
 Morgenstern, M Munsterkotter, S Rudd,  Weil
... mewes@gsf.de. ACKNOWLEDGEMENTS We thank V. Solovyev (Softberry Inc., NY)
for providing and tuning the FGENSH program. This work was ...
Molecular Plant-Microbe Interactions
February 2002, Volume 15, Number 2
Pages 120-128
DOI: 10.1094/MPMI.2002.15.2.120
CPR1: A Gene Encoding a Putative Signal Peptidase That Functions in Pathogenicity of Colletotrichum graminicola to Maize
M. R. Thon, E. M. Nuckles, J. E. Takach, and L. J. Vaillanc
Department of Plant Pathology, S-305 Agricultural Sciences Center-North, University of Kentucky, Lexington 40546-0091, U.S.A.
... on-line from The Sanger Center's Computational Genomics Group); and a version of
FGENESH trained on N. crassa sequences (available on-line from Softberry, Inc ...
Fungal Genetics and Biology
Volume 36, Issue 3, August 2002, Pages 234-241
Size and complexity of the nuclear genome of the ectomycorrhizal fungus Paxillus involutus
Quere, Tomas Johansson and Anders Tunlid
Department of Microbial Ecology, Lund University, Ecology Building, S-223 62, Lund, Sweden
... gatech.edu/GeneMark/), the GlimmerM (www.tigr.org/softlab/glimmerm/), the ORF finder
(www.ncbi.nlm.nih.gov/gorf/), and the FgeneSH (www.softberry.com/nucleo ...
Drug discovery today
Vol. 7, No. 11 (Suppl.), 2002, S70-S76
www.drugdiscoverytoday.com
Genome annotation techniques: new approaches and challenges
Alistair G. Rust Emmanuel Mongin and *Ewan Birney
European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus Hinxton Cambridge UK CB10 1SD
... Examples of such prediction programs include Genscan [14] (used by Celera, ORNL
and Ensembl), FGENESH [15] (used in the Softberry and UCSC browsers as well as ...
Box 1. Useful human genome annotation and browser URLs
Human genome browsers
o UCSC Human Genome Browser: http://genome.cse.ucsc.edu/cgi-bin/hgGateway/
o Softberry Genome Explorer: http://www.softberry.com/berry.phtml?topic=genomexp
Ab initio gene prediction programs. Ab initio gene predictors rely on the statistical qualities of exons rather than on homologies. Examples of such prediction programs include Genscan [14] (used by Celera, ORNL and Ensembl), FGENESH [15] (used in the Softberry and UCSC browsers as well as Celera's pipeline) and GrailEXP [16] (ORNL).
Proc Natl Acad Sci U S A.
2002 August 20; 99(17): 11423-11428.
Identification of G protein-coupled receptors for Drosophila PRXamide peptides, CCAP, corazonin, and AKH supports a theory of ligand-receptor coevolution
Yoonseong Park,* Young-Joon Kim*, and Michael E. Adams*,
Departments of *Entomology and Cell Biology and Neuroscience, 5429 Boyce Hall,
University of California, Riverside, CA 92521
...For each Drosophila GPCR, prediction of gene structure was made in FGENESH (www.softberry.com; ref. 21) by using about 20 kb of genomic sequence surrounding highly conserved regions, particularly for 5 prime and 3 prime ends of ORFs.
Putative Drosophila GPCRs in the database were amplified by RT-PCR using primers based on gene predictions in the FGENESH gene finder (www.softberry.com; ref. 21).
21. Salamov A. A. & Solovyev, V. V. (2000) Genome Res. 10, 516-522....
Eukaryotic Cell,
October 2002, p. 719-724, Vol. 1, No. 5
Isocitrate Lyase Is Essential for Pathogenicity of the Fungus Leptosphaeria maculans to Canola (Brassica napus)
Alexander Idnurm and Barbara J. Howlett*
School of Botany, The University of Melbourne, Melbourne, Victoria 3010, Australia
... The DNA sequence obtained was compared to those in the GenBank database by using BLAST (1), and genes were predicted by using FGENESH software (http://www.softberry.com) and GENSCAN (www.bionavigator.com).
Biotech Software & Internet Report
November 2002, 3(5-6): 151-153. doi:10.1089/152791602321105834.
News
... sequence data. The genes are identified with the FGENESH11 gene modeling software
exclusively li- censed from Softberry, Inc. Automatic ...
Genome
2002 Oct;45(5):963-72.
Analysis of 106 kb of contiguous DNA sequence from the D genome of wheat reveals high gene density ...
SA Brooks, L Huang, BS Gill, JP Fellers
Department of Plant Pathology, Kansas State University, Manhattan 66506, USA.
... trix. In addition, FGENESH 1.1 (http://www.softberry.com) was used for CDS prediction with monocot genomic DNA parameters. Both ...
Molecular Genetics and Genomics
Issue: Volume 267, Number 6 Date: August 2002 Pages: 713 - 720
Genome sequencing of a 239-kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast DNA insertion
Q. Yuan, J. Hill, J. Hsiao, K. Moffat, S. Ouyang, Z. Cheng, J. Jiang, C. Buell
A1 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
A2 Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
... The sequences were analyzed with several gene prediction programs, including FGENESH (http://www.softberry.com), Genemark.hmm (rice matrix; http://opal.biology ...
Genetics,
Vol. 162, 1389-1400, November 2002, Copyright © 2002
Different Types and Rates of Genome Evolution Detected by Comparative Sequence Analysis of Orthologous Segments From Four Cereal Genomes
Wusirika Ramakrishna et al
a Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907,
FGENESH (http://www.softberry.com/nucleo.html) with the maize training set was used for gene prediction in addition to GENSCAN (http://genes.mit.edu/GENSCAN.html) and GeneMark.hmm (http://genemark.biology.gatech.edu/Gene Mark/).
Nature
420, 316 - 320 (21 November 2002) | doi:10.1038/nature01183
Sequence and analysis of rice chromosome 4
Feng et al
National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
Chinese National Human Genome Center at Shanghai, 351 Guo Shoujing Road, Shanghai 201203, China
FGENESH used for annotation of rice chromosome 4.
Functional & Integrative Genomics
Issue: Volume 2, Numbers 1-2 Date: May 2002 Pages: 51 - 59
Genomic sequencing reveals gene content, genomic organization, and recombination relationships in barley
Nils Rostoks et al
A1 Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
... version 1.0 with maize parameters. The FGENESH predictions were run at http://www.softberry.com/. BAC genomic regions were defined ...
Genome
2003 Dec;46(6):1084-97
Structural organization of the barley D-hordein locus in comparison with its orthologous regions of wheat genomes
Gu et al.,
United States Department of Agriculture, Agriculture Research Service, Western Regional Research Center, Albany, CA 94710, USA
... et al. 1997) to search for additional genes. In addition, FGENESH (http://www.softberry.com/berry.phtml) and. GENESCAN (http://genes ...
PNAS
July 9, 2002 vol. 99 no. 14 9328-9333
The barley stem rust-resistance gene Rpg1 is a novel disease-resistance gene with homology to receptor kinases
R. Brueggeman et al
* Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420; Department of Plant Pathology, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108-6030; and School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4234
.. The gene prediction programs GENSCAN (http://genes.mit.edu/GENSCAN.html) and FGENESH (http://www.softberry.com), as well as NEURAL NETWORK PROMOTER PREDICTION (http://www.fruitfly.org/seq_tools/promoter.html) localized the putative transcription start site of the gene about 400 bp upstream of the translation start site.
Plant Physiol.
2002 December; 130(4): 1626-1635.
Contiguous Genomic DNA Sequence Comprising the 19-kD Zein Gene Family from Maize1
Rentao Song and Joachim Messing*
Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, New Jersey 08854-8020
.. Draft sequences generated from high-throughput DNA sequencing (phase II) were subjected to gene prediction programs with FGENESH (Softberry, Inc., Mount Kisco, NY).
The Plant Cell,
Vol. 14, 3213-3223, December 2002,
Structural Analysis of the Maize Rp1 Complex Reveals Numerous Sites and Unexpected Mechanisms of Local Rearrangement
Wusirika Ramakrishnaa, John Embertona, Matthew Ogdena, Phillip SanMiguelb and Jeffrey L. Bennetzen1,a
a Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
b Purdue University Genomics Core, Purdue University, West Lafayette, Indiana 47907
... FGENESH (http://www.softberry.com/berry.phtml) with the monocot training set was
used for gene prediction, in addition to GENSCAN (http://genes.mit.edu/GENSCAN ...
Plant Physiol.
2002 December; 130(4): 1728-1738.
Comparative Sequence Analysis of the Sorghum Rph Region and the Maize Rp1 Resistance Gene Complex
Wusirika Ramakrishna, John Emberton, Phillip SanMiguel, Matthew Ogden, Victor Llaca, Joachim Messing, and Jeffrey L. Bennetzen
Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907 (W.R., J.E., M.O., J.L.B.); Purdue University Genomics Core, Purdue University, West Lafayette, Indiana 47907 (P.S.M.); and Waksman Institute, Rutgers University, Piscataway, New Jersey 08854 (V.L., J.M.)
...Annotation and sequence analysis were performed as described earlier (Dubcovsky et al., 2001 ; Song et al., 2001 ; Ramakrishna et al., 2002a ). FGENESH (http://www.softberry.com/berry.phtml) with the monocot training set was used for gene prediction in addition to GENSCAN (http://genes.mit.edu/GENSCAN.html) and GeneMark.hmm (http://opal.biology.gatech.edu/GeneMark/eukhmm.cgi).
Rapid Genome Evolution Revealed by Comparative Sequence Analysis of Orthologous Regions from Four ...
YQ Gu, D Coleman-Derr, X Kong, OD Anderson
... FGENESH (http://www.softberry.com/nucleo.html) and GENESCAN (http://genemark.
mit.edu/GENESCAN.htm) were used for gene prediction. ...
Nature
419, 755 - 755 (17 Oct 2002) Technology Feature
Putting a name on it
Marina Chicurel
...used in the landmark publications of the draft human genome sequence. FGENESH, produced by software firm Softberry of Mount Kisco, New York,
proved particularly useful for the Syngenta-led annotation of the rice genome sequence. Good...
PLoS ONE
2012, 7(9): e44264. doi:10.1371/journal.pone.0044264
Identification and Sequence Analysis of Metazoan tRNA 3?-End Processing Enzymes tRNase Zs.
Wang et al.,
Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
... The splicing pattern was verified using the Fgenesh and Fgenesh_GC programs provided at the Softberry website (http://linux1.softberry.com/berry.phtml??topic=fgenesh). ...
BMC Evolutionary Biology
2011, 11:219 doi:10.1186/1471-2148-11-219
A survey of green plant tRNA 3'-end processing enzyme tRNase Zs, homologs of the candidate prostate cancer susceptibility protein ELAC2
Fan et al.,
1 Laboratory of Yeast Genetics and Molecular Biology, School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
2 Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
...The splicing pattern was verified using the FGENESH and FGENESH_GC programs provided at the Softberry website...
Gene
Volume 451, Issues 1-2, 1 February 2010, Pages 6-14 doi:10.1016/j.gene.2009.08.018
Expression and regulation of IL-22 by bovine peripheral blood g/d T cells
Shi-Dong Ma, Cheryl A. Lancto, Shinichiro Enomoto, Mitchell S. Abrahamsen and Mark S. Rutherford
Department of Veterinary and Biomedical Sciences, University of Minnesota, 1988 Fitch Avenue, Room 295 AS/VM, St. Paul, MN 55108, USA
.. Genomic structure was deduced using FGENSH_GC program at http://www.softberry.com/berry.
phtml?topic=fgeneshgc&group=programs&subgroup=gfind, and cDNA-genomic nucleotide
sequences were aligned using Blast2 at http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2 ..
Nucleosides, Nucleotides and Nucleic Acids
Volume 32, Issue 10, 2013 pages 529-554 DOI:10.1080/15257770.2013.832773
Gene Identification Programs in Bread Wheat: A Comparison Study
Nasiri et al.,
a Department of Agronomy and Plant Breeding, Division of Molecular Plant Genetics, College of Agricultural & Natural Resources , University of Tehran , Karaj , Tehran , Iran
b Department of Plant Biotechnology, College of Agricultural & Natural Resources , University of Tehran , Karaj , Tehran , Iran
... Ab initio gene finding in Drosophila genomic DNA. Genome Res., 10: 391–393. [CrossRef],
[PubMed] View all references ] is an HMM-based variant of Fgenes that can be easily utilized
online at softberry web server (http://linux1.softberry.com/berry.phtml). ...
Developmental & Comparative Immunology
Volume 34, Issue 2, February 2010, Pages 114-122 doi:10.1016/j.dci.2009.08.011
Presence of an unique IgT on the IGH locus in three-spined stickleback fish (Gasterosteus aculeatus) and the very recent generation of a repertoire of VH genes
Francisco Gambon-Deza a, b, Christian Sanchez-Espinelb, 1, and Susana Magadan-Mompoc, 2,
a Unidad de Inmunologia, Hospital do Meixoeiro, Carretera de Madrid s/n, Vigo 36210, Pontevedra, Spain
b Shared Unity of Immunology, University of Vigo - Vigo University Hospital Complex (Hospital Meixoeiro), Edificio de Ciencias Experimentales, Rua das Abeleiras, Campus As Lagoas-Marcosende, Vigo 36310, Pontevedra, Spain
... immunoglobulin mRNAs. Limits of antibodies that were not yet published were
deduced following the instructions in the software FGENES (www.softberry.com) and
Augustus (http://augustus.gobics.de/submission). The results ...
J Mol Diagn.
2010 Jul;12(4):520-4. Epub 2010 May 27
Comprehensive characterization of a novel intronic pseudo-exon inserted within an e14/a2 BCR-ABL rearrangement in a patient with chronic myeloid leukemia
Sorel et al.,
Service Service d'Hematologie et Oncologie Biologique - INSERM U935, Centre Hospitalier Universitaire de Poitiers, 2, rue de la Miletrie, 86021 Poitiers Cedex, France.
... Georgia Institute of Technology, Atlanta, GA; version 3.0; 2005; available at http://exon.gatech.
edu/GeneMark/; accessed October 14, 2009), 6 and FGENES (SoftBerry, Mount Kisco, NY; 2007;
available at http://linux1.softberry.com/berry.phtml; accessed October 14, 2009 ...
Molecular Immunology
Volume 46, Issue 13, August 2009, Pages 2515-2523
The immunoglobulin heavy chain locus in the platypus (Ornithorhynchus anatinus)
F. Gambon-Deza, C. Sanchez-Espinel and S. Magadan-Mompo
aUnity of Inmunology, Vigo University Hospital Complex (CHUVI), Carretera de Madrid s/n., 36210 Vigo, Pontevedra, Spain
bArea of Immunology, Faculty of Biology, University of Vigo, Department of Biochemistry, Genetics and Immunology, Rua das Abeleiras, Campus As Lagoas-Marcosende, 36310 Vigo, Pontevedra, Spain
... Limits of antibodies that were not yet published (IGHD and IGHY) were deduced following the
instructions in the software FGENES (www.softberry.com) and Augustus (http://augustus.gobics.
de/submission) together with the results obtained upon comparison with the reptilian ...
Developmental & Comparative Immunology
Volume 34, Issue 2, February 2010, Pages 114-122
Presence of an unique IgT on the IGH locus in three-spined stickleback fish (Gasterosteus aculeatus) and the very recent generation of a repertoire of VH genes
F. Gambon-Deza, C. Sanchez-Espinel and S. Magadan-Mompo
a Unidad de Inmunologia, Hospital do Meixoeiro, Carretera de Madrid s/n, Vigo 36210, Pontevedra, Spain
... immunoglobulin mRNAs. Limits of antibodies that were not yet published were
deduced following the instructions in the software FGENES (www.softberry.com) and
Augustus (http://augustus.gobics.de/submission). The results ...
Food and Chemical Toxicology
Volume 46, Issue 4, April 2008, Pages 1249-1256
SULT1C3, an orphan sequence of the human genome, encodes an enzyme activating various promutagens
Walter Meinl, Claudia Donath, Heiko Schneider Yasmin Sommer and Hansruedi Glat
German Institute of Human Nutrition (DIfE) Potsdam-Rehbru"cke, Department of Nutritional Toxicology, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
... SULT1 genes. No BLAST hit was observed for exon 4. It was found with the
FGENES algorithm (hosted by http://www.softberry.com). Its ...
Acta Phytopathologica et Entomologica Hungarica
Volume 43, Number 1/June 2008 pp. 1-13
Cloning and characterization of a HOG-type MAP kinase encoding gene from Fusarium proliferatum
A. L. Adam, G. Kohut, L. Hornok
Szent Istvan University Agricultural Biotechnology Center, Mycology Group of the Hungarian
Academy of Sciences, Institute of Plant Protection Pater K. u. 1 H-2103 Godollo Hungary
... Se- quence data were analyzed with the Lasergene (DNAStar Inc., USA) software
package and the FGENES program (http://www.softberry.com). ...
Plant Pathology
Volume 57 Issue 5, Pages 861 - 869 Published Online: 21 Mar 2008
Peroxidases in the early responses of different potato cultivars to infection by Potato virus YNTN
M. Milavec, K. Gruden, M. Ravnikar, M. Kovac
National Institute of Biology, Vecna pot 111, 1000 Ljubljana, Slovenia
... Intron/exon structure of the gene was determined using FGENES 1·0, available
online from SoftBerry (http://www.softberry.com/berry.phtml). ...
J. Biol. Chem.,
Vol. 281, Issue 40, 29753-29761, October 6, 2006
Regulation of Hypocretin (Orexin) Expression in Embryonic Zebrafish*
Juliette H. Faraco et al.,
Stanford University Center for Narcolepsy, Department of Psychiatry
and Behavioral Sciences, Stanford University, Stanford, California 94305,
the Howard Hughes Medical Institute, Stanford University, Stanford,
California 94305, and INSERM, U784, 75230 Paris, France
... rate options. Fgenes, Fex, and Spl (Softberry.com) were used to identify
potential first exons and/or splice donor sites. Signal ...
Cellular & Molecular Biology Letters
Volume 11, Number 2 / June, 2006 pp. 214-229
En/Spm-like transposons in Poaceae species: Transposase sequence variability and chromosomal distribution
Ahu Altinkut, Olga Raskina, Eviatar Nevo and Alexander Belyayev
Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, 31905, Israel
... The TPase open reading frame was assembled by removing introns using the FGENES 2.0 Program
(http://www.softberry.com/berry.phtml?topic=fgenesh&group ...
Neuron
Volume 50 (2006), Issue 5, Pages 683-695
The Myotomal diwanka (lh3) Glycosyltransferase and Type XVIII Collagen Are Critical for Motor Growth Cone Migration
V. Schneider, M. Granato
University of Pennsylvania School of Medicine, Department of Cell and Developmental Biology, Philadelphia, Pennsylvania 19104
... Open reading frames within the diwanka interval were predicted with Genscan
(http://genes.mit.edu/GENSCAN.html) and Fgenes (http://www.softberry.com/berry.phtml ...
Bioinformatics
2005 21(9):1776-1781; doi:10.1093/bioinformatics/bti283
Gene finding for the helical cytokines
Darrell Conklin 1,*, Betty Haldeman 2 and Zeren Gao 2
1Department of Computing, City University London, United Kingdom
2ZymoGenetics Inc. Seattle, USA
... For comparison purposes, three other gene finding methods were also run on the same
dataset: Fgenes v1.6 (Solovyev et al., 1994), Genscan v1.0 (Burge and Karlin ...
Genes, Chromosomes and Cancer
Volume 43, Issue 1 , Pages 83 - 94 Published Online: 18 Feb 2005
Molecular cloning and characterization of FBXO47, a novel gene containing an F-box domain, located in the 17q12 band deleted in papillary renal cell carcinoma
Barbara Simon-Kayser et al
1Laboratoire d'Etude du Polymorphisme de l' ADN, Faculte de Medecine, Nantes, France
... html), GrailExp (http://grail.Isd.ornl.gov/grailexp), Fgenes (http://genomic.sanger.
ac.uk/gf/gf.shtml), and Genmark (http://www2.ebi.ac.uk/genemark). ...
Journal of Neurobiology
Volume 63, Issue 3 , Pages 235 - 254 Published Online: 4 Mar 2005
Shaw potassium channel genes in Drosophila
James J. L. Hodge 1 2, James C. Choi 2, Cahir J. O'Kane 1 *, Leslie C. Griffith 2
1Department of Genetics, University of Cambridge, Downing Site, Cambridge CB2 3EH, United Kingdom
2Department of Biology and Volen Center for Complex Systems, Brandeis University MS008, 415 South Street, Waltham, Massachusetts 02454-9110
... Intron/exon structure of Shawl was initially predicted using the Fgenes program
(Salamov and Solovyev, 2000) on the Baylor College of Medicine Genefinder ...
Current Proteomics,
January 2004, vol. 1, no. 1, pp. 41-48(8)
Annotation of the Human Genome by High-Throughput Sequence Analysis of Naturally Occurring Proteins
Authors: McGowan S.J.1; Terrett J.1; Brown C.G.1; Adam P.J.1; Aldridge L.1; Allen J.C.1; Amess B.1; Andrews K.A.1; Barnes M.1; Barnwell D.E.1
Affiliations: 1: Oxford GlycoSciences plc, The Forum, 86 Milton Park, Abingdon, OX14 4RY, UK.
... The polymorphic 'hypothetical transcriptome' was cons- tructed from transcripts predicted by Fgenes, FGENESH (Softberry Inc, Mount Kisco, NY, USA), GENSCAN ...
Nature Biotechnology
22, 1146 - 1149
5'-end SAGE for the analysis of transcriptional start sites
Hashimoto et al. (2004)..
...from expressed sequence tag (EST) maps, analysis of full-length cDNAs and computational annotation by Genscan, Genie, Fgenes and other programs.
Hemoglobin
Volume 28, Number 3 / 2004 255 - 259
An a-Thalassemia Phenotype in a Dutch Hindustani, Caused by a New Point Mutation that Creates an Alternative Splice Donor Site in the First Exon of the a2-Globin Gene
Cornelis L. Harteveld A1, Pierre W. Wijermans A2, Peter van Delft A1, Ellen Rasp A2, Hans L. Haak A2, Piero C. Giordano A1
A1 Hemoglobinopathies Laboratory, Leiden University Medical Center, PO Box 9503, 2300, Leiden, The Netherlands
A2 Leyenburg Hospital, The Hague, The Netherlands
... and GRAIL/ gap2 (Gene Recognition and Assembly Internet Link, Sequence exploration
and gene discovery Version 1.3), Genefinder, GENSCAN, Fgenes and HMMGene ...
Journal of Medical Genetics
2004;41:e52
Genomic organisation of the UDP-N-acetylglucosamine-1-phosphotransferase gamma subunit (GNPTAG) and its mutations in mucolipidosis III
A Raas-Rothschild et al
1 Department of Human Genetics, Hadassah University Medical Center, Jerusalem, Israel
... third intron is 9 kb. This structure was consistent with the exon prediction
of fgenes and Genscan. Each splice donor and acceptor ...
Current Biology
2004, Volume 14, Issue 19, Pages R832-R833
Dual capacity of a human olfactory receptor
M. Spehr, K. Schwane, S. Heilmann, G. Gisselmann, T. Hummel, H. Hatt
... (B) RT-PCR with intron spanning primers. Candidates for 5'UTR exons were identified
using FGENES and FEX software (SoftBerry, Mount Kisco, NY). ...
Molecular Biology Reports
Volume 40, Issue 2 , pp 1201-1210 DOI: 10.1007/s11033-012-2162-2
Characterization of a vacuolar zinc transporter OZT1 in rice (Oryza sativa L.)
Lan et al.,
1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China
... genome database in GenBank with tblastn program. The identified homologous
sequence was further analyzed for predicting the complete ORF with FGENES-M
program (http://www.softberry.com). To verify the accuracy of gene ...
Molecular Biology Reports
Volume 36, Number 2 / February, 2009, pp. 281-287, DOI:10.1007/s11033-007-9177-0
Cloning and functional identification of two members of the ZIP (Zrt, Irt-like protein) gene family in rice (Oryza sativa L.)
Xia Yang 1, Ji Huang 1, Yan Jiang 1 and Hong-Sheng Zhang 1
(1) State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
... of China through tBLASTn algorithm program. The cDNA sequences of two putative
rice ZIP genes with a complete ORF were assembled using FGENES-M program
(http://www.softberry.com). Accord- ing to the predicted sequence ...
Molecular Biology Reports
Volume 35, Number 2 / June 2008 pp. 145-152
Molecular cloning and characterization of a novel SNAP25-type protein gene OsSNAP32 in rice ( Oryza sativa L.)
Yong-Mei Bao, Jian-Fei Wang, Ji Huang and Hong-Sheng Zhang
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
... The genome organization and chromo- some mapping of the OsSNAP32 were investigated
by the software FGENES-M at Softberry (http://www.softberry. ...
Molecular Genetics and Genomics
Volume 279, Number 3 / March, 2008 Pages 291-301
Cloning and characterization of three genes encoding Qb-SNARE proteins in rice
Yong-Mei Bao1, Jian-Fei Wang1, Ji Huang1 and Hong-Sheng Zhang
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
... The genome organization of three OsNPSNs were investigated using FGENES-M software
(http://www.softberry.com/berry.phtml) by comparing the cloned cDNAs with ...
Gene
Volume 415, Issues 1-2, 31 May 2008, Pages 1-12
Expression analysis of the calcineurin B-like gene family in rice (Oryza sativa L.) under environmental stresses
Zhimin Gu et al.,
State key lab of crop genetics and germplasm enhancement, Nanjing Agricultural University, Nanjing, 210095, PR China
College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, PR China
... Fgenes-M (http://www.softberry.com), Genscan (http://genes.mit.edu/GENSCAN.html),
BlastP (http://www.ncbi.nlm.nih.gov/BLAST/), National Centre for ...
Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
Volume 1769, Issue 4, April 2007, Pages 220-227
A novel rice C2H2-type zinc finger protein lacking DLN-box/EAR-motif plays a role in salt tolerance
Ji Huang1, a, Xia Yang1, a, Mei-Mei Wang2, a, Hai-Juan Tanga, Ling-Yun Dinga, Yin Shena and Hong-Sheng Zhang, a,
aState Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
... probe sequence. The putative ORFs for these sequences were predicted with
FGENES-M program (http://www.softberry.com). ZFP182, one ...
BMC Bioinformatics.
2005; 6: 25.
Integrating alternative splicing detection into gene prediction
Sylvain Foissac1 and Thomas Schiex1
1Unite de Biometrie et Intelligence Artificielle, INRA, 31326 Castanet Tolosan, France
..This approach has been applied eg. in HMMgene or in FGENES-M (unpub.)...
Molecular Biology Reports
Volume 32, Number 3 / September, 2005 pp.177-183
Rice ZFP15 Gene Encoding for a Novel C2H2-type Zinc Finger Protein Lacking DLN box, is Regulated by Spike Development but not by Abiotic Stresses
Ji Huang1, Jianfei Wang1 and Hongsheng Zhang1
(1) State Key Laboratory of Crop Genetics and Germplasm Enhancement, Rice Research Institute, Nanjing Agricultural University, Nanjing, 210095, China
... sequence. These sequences were analyzed with FGENES-M program (http://www.
softberry.com) for predict- ing the complete ORFs. The ...
DNA Sequence - The Journal of Sequencing and Mapping
Volume 15, Number 1 / February 2004 39 - 43
Isolation and Characterization of Two cDNAs Encoding Translation Initiation Factor 1A from Rice(Oryza sativa L.)
Ji Huang, Jianfei Wang, Shengping Qiu, Hongsheng Zhang
State Key Laboratory of Crop Genetics and Germplasm Enhancement Rice Research Institute Nanjing Agricultural University 210095 Nanjing People's Republic of China
... Then the ORF without introns was assembled based on the sequence of each scaffold
using the program FGENES-M (http://www. softberry.com). ...
Plant Science
Volume 169, Issue 3, September 2005, Pages 470-477
Cloning and characterization of a novel rice gene family encoding putative dual-specificity protein kinases, involved in plant responses to abiotic and biotic stresses
Zhimin Gu, Jianfei Wang, Ji Huang and Hongsheng Zhang
National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Department of Agronomy, Nanjing 210095, China
... genomic contigs having higher homology with the probe were obtained for prediction
and assembling of putative ORFs by FGENES-M program (http://www.softberry.co
Applied microbiology and biotechnology
2015, 99(4), 1719-1730. DOI: 10.1007/s00253-014-5999-6
C7-prenylation of tryptophanyl and O-prenylation of tyrosyl residues in dipeptides by an Aspergillus terreus prenyltransferase
Wunsch, C., Zou, H. X., Linne, U., Li, S. M
1. Institut fur Pharmazeutische Biologie und Biotechnologie, Philipps-Universitat Marburg, Deutschhausstra?e 17A, 35037, Marburg, Germany
2. Zhejiang Provincial Key Lab for Subtropical Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People’s Republic of China
... 2013) or purchased from Bachem (Bubendorf, Switzerland). Computer-assisted sequence analysis
Sequence analysis and intron prediction were performed with FGENESH-M (Softberry, Mount
Kisco, NY; www.softberry. com) and geneid (http://genome.crg.es/geneid.html). Fig. ...
Jurnal Teknologi
2015, 77(24). DOI: http://dx.doi.org/10.11113/jt.v77.6727
Annotations and domain analysis of polyketide synthase genes in fungal wheat pathogen, mycosphaerella graminicola
Khalid, R. M., Bailey, A., & Cox, R. J.
... The presence of introns were determined using Softberry tools [18], because up to now,
there is no cDNA of a complete M. graminicola PKS gene. ... [18] http://linux1.softberry.com/
berry.phtml?topic=fgenesh-m&group=programs&subgroup=gfind. ...
Applied microbiology and biotechnology, 1-11.
2014, 1-11. DOI: 10.1007/s00253-014-5872-7
A new member of the DMATS superfamily from Aspergillus niger catalyzes prenylations of both tyrosine and tryptophan derivatives.
Fan A. et al.,
1. Institut fur Pharmazeutische Biologie und Biotechnologie, Philipps-Universitat Marburg, Deutschhausstrasse 17A, 35037, Marburg, Germany
2. Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, China
... nlm.nih.gov). DNASIS software package (version 2.1; Hitachi Software Engineering,
Tokyo, Japan) and FGENESH-M (Softberry, Mount Kisco, NY; www.softberry. com) were
used for sequence analysis and intron prediction, respectively. ...
BMC plant biology
(2013). 13(1), 176. DOI:10.1186/1471-2229-13-176
An apple MYB transcription factor, MdMYB3, is involved in regulation of anthocyanin biosynthesis and flower development
Vimolmangkang, S., Han, Y., Wei, G., & Korban, S. S.
1 Department of Natural Resources and Environmental Sciences, University of Illinois, 1201 W. Gregory, Urbana, IL 61801, USA
2 Department of Pharmacognosy, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
... Recovery of cDNA sequence encoding MdMYB3 in apple The genomic sequences
encoding MdMYB3 were analyzed using FGENESH-M program (http://www. softberry.
com), and an open reading frame (ORF) was predicted. ...
J. Exp. Bot.
(2012) 63 (1): 471-488.
doi: 10.1093/jxb/err295
Two SERK genes are markers of pluripotency in Cyclamen persicum Mill.
Savona et al.,
1‘Sapienza’ University of Rome, Dept. of Environmental Biology, Rome, Italy
2‘Sapienza’ University of Rome, Dept. of Biology and Biotechnology, Rome, Italy
... programs (http://www.expasy.org/prosite/). ORFs were found with FGENESH-M
(fgenesh-m; http://linux1.softberry.com/berry.phtml?topic=fgenesh-m&group=
programs&subgroup=gfind). Phylogenetic analysis was performed by ...
Med. Chem. Commun.
2012,3, 987-996 DOI: 10.1039/C2MD20029E
Comparative analysis of the biosynthetic systems for fungal bicyclo[2.2.2]diazaoctane indole alkaloids: the (+)/(?)-notoamide, paraherquamide and malbrancheamide pathways
Shengying Li et al.,
... Phq protein). a Genes were predicted using the FGENESH-M tool from
http://www.softberry.com; functions of gene products were predicted using BLAST
search.b -: Homology cannot be calculated due to unrelatedness. NotA ...
J. Proteome Res.
2011, 10 (10), pp 4478–4504
DOI: 10.1021/pr200284e
Genomics, Transcriptomics, and Peptidomics of Daphnia pulex Neuropeptides and Protein Hormones
Dircksen et al.,
Department of Zoology, Stockholm University, Sweden
Institute of Zoology, University of Cologne, Cologne, Germany
Department of Biology, K.U. Leuven, Belgium
... More detailed analyses and novel annotations of genes, their exon-intron boundaries were
performed usually with aid of Fgenesh-M gene finding tools (Softberry Inc., Mount Kisco, NY;
http://linux1.softberry.com/berry.phtml?topic=fgenesh-m&group=programs&subgroup=gfind ...
Biochemical and Biophysical Research Communications
Volume 354, Issue 3, 16 March 2007, Pages 668-675
Sp-tetraKCNG: A novel cyclic nucleotide gated K+ channel
Blanca Estela Galindo, Jose Luis de la Vega-Beltran, Pedro Labarca, Victor D. Vacquier and Alberto Darszon
Depto. de Genetica del Desarrollo y Fisiologia Molecular del Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Apdo Postal 510-3, Cuernavaca, Morelos 62271, Mexico
... 3?-RACE was performed to obtain the 3?-end, and the 5?-end (684 nucleotides) was
predicted by FGENESH-M, a program at the Softberry website (http://www ...
DNA Sequence - The Journal of Sequencing and Mapping
Volume 17, Number 1 / February 2006 pp. 24 - 30
Isolation and characterization of a new Na+/H+ antiporter gene OsNHA1 from rice (Oryza sativa L.)
Zhou et al.,
Nanjing Agricultural University, State key laboratory of crop genetics and germplasm enhancement, Nanjing, 210095, China
... An expected cDNA sequence containing a complete open reading frame (ORF)
was predicted using FGENESH-M program (http://www.softberry. ...
Metabolic engineering
2015, 29, 97-105. http://dx.doi.org/10.1016/j.ymben.2015.03.003
Production of bioactive ginsenosides Rh2 and Rg3 by metabolically engineered yeasts
Wang, P. et al.,
a CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
b State Key Laboratory of Drug Research, Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201203, China
... Yan et al., 2014). The BESTORF software (http://linux1.softberry.com/berry.phtml?
topic=bestorf&group=programs&subgroup=gfind) was used for prediction of ORFs
in cDNA sequences in the database. ORFs encoding UDP ...
BMC Genomics
2013, 14:695 doi:10.1186/1471-2164-14-695
Histoplasma yeast and mycelial transcriptomes reveal pathogenic-phase and lineage-specific gene expression profiles
Edwards et al.,
1 The Department of Microbiology, Ohio State University, 484 W. 12th Ave., Columbus, OH 43210, USA
2 The Department of Microbial Infection and Immunity, Ohio State University, 484 W. 12th Ave., Columbus, OH 43210, USA
... Separately, the RNA-seq short reads were assembled into transcript contigs de novo (ie,
independent of the reference genome sequence) using Inchworm [39] and open reading frames
extracted from the transcripts with BestORF (Molquest package, Softberry). ...
PloS one
September 02, 2013DOI: 10.1371/journal.pone.0073560
Evolutionary History of Chordate PAX Genes: Dynamics of Change in a Complex Gene Family
Vanessa Rodrigues Paixao-Cortes, Francisco Mauro Salzano, Maria Catira Bortolini
Departamento de Genetica and Programa de Pos-Graduacao em Genetica e Biologia Molecular, Instituto de Biociencias, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
... The genomic sequences of possible unannotated orthologs were verified using three programs
that can predict open reading frames (ORF): BESTORF (http://linux1.softberry.com/berry.phtml??
topic=bestorf&group=programs&subgroup=gf?ind), GeneWise (http://www.ebi.ac.uk ...
Nature Biotechnology
30, 549–554 (2012) doi:10.1038/nbt.2195
Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential
Zhang et al.,
BGI-Shenzhen, Chinese Ministry of Agriculture, Key Lab of Genomics, Shenzhen, China.
... Open reading frames (ORFs) were predicted using BESTORF (http://linux1.softberry.com/berry.phtml?topic=bestorf&group=programs&subgroup=gfind) with parameters trained on monocot genes without filtering of UTRs. ...
Phytopathology
August 2012, Volume 102, Number 8
Pages 741-748
http://dx.doi.org/10.1094/PHYTO-02-12-0021-R
Role of the Pathotype-Specific ACRTS1 Gene Encoding a Hydroxylase Involved in the Biosynthesis of Host-Selective ACR-Toxin in the Rough Lemon Pathotype of Alternaria alternata
Izumi et al.,
Faculty of Agriculture, Kagawa University, Miki, Kagawa 761-0795 Japan; Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430.
... Shimadze, Tsukuba, Japan). Putative open reading frames (ORFs) were identified
using BESTORF (http://linux1.softberry. com/berry.phtml) from the sequence of the
respective contigs by mass sequencing. Transcripts of ACRTS1 ...
Fungal Genetics and Biology
Volume 49, Issue 6, June 2012, Pages 470–482 DOI: 10.1016/j.fgb.2012.04.001
Transcriptome analysis of enriched Golovinomyces orontii haustoria by deep 454 pyrosequencing
We?ling et al.,
a Max-Planck-Institute for Plant Breeding Research, Department of Plant–Microbe Interactions, Carl-von-Linne-Weg 10, 50829 Cologne, Germany
b Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin-Dahlem, Germany
... Open reading frames were predicted from these contigs using BestORF with the Sclerotinia
sclerotiorum matrix (Softberry, Mount Kisco, NY, USA). Predicted proteins were then
annotated by Blast2Go (Conesa et al. 2005) using default parameters. ...
PLoS Pathog
8(4): e1002643. doi:10.1371/journal.ppat.1002643
Sequential Delivery of Host-Induced Virulence Effectors by Appressoria and Intracellular Hyphae of the Phytopathogen Colletotrichum higginsianum.
Kleemann et al.,
Department of Plant-Microbe Interactions, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany
Central Microscopy Max-Planck-Institute for Plant Breeding Research, Cologne, Germany
...ORFs were predicted from EST contigs with the Fusarium matrix of BESTORF (Molquest package, Softberry). ...
Nature
479, 529–533 (24 November 2011) doi:10.1038/nature10553
Ascaris suum draft genome
Jex et al.,
Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria 3010, Australia
BGI-Shenzhen, Shenzhen, 518083, China
...The open reading frame of each gene was predicted using BestORF (http://www.softberry.com). ...
PLoS ONE
2011, 6(2): e14697. doi:10.1371/journal.pone.0014697
ENCODE Tiling Array Analysis Identifies Differentially Expressed Annotated and Novel 5? Capped RNAs in Hepatitis C Infected Liver.
Folkers et al.,
Department of Medicine, University of Utah, Salt Lake City, Utah, United States of America
Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
...The use of a sequence analysis tool (BESTORF, www.softberry.com) to predict potential coding fragments in these unannotated sequences,...
MAKARA OF SCIENCE SERIES,
VOL 15, NO 2 (2011)
ISOLATION, CLONING AND CHARACTERIZATION OF ACTIN-ENCODING CDNAS FROM JATROPHA CURCAS L. IP-2P
Ratna Yuniati, Utut Widyastuti, Didy Sopandie, Akiho Yokota, Suharsono
... tool) (http://www.ncbi.nlm.nih. gov/BLAST/) program. The analysis of open reading
frame (ORF) was carried out by using BESTORF program (http://www.softberry/bestorf/
htm). Phylogenetic analyses were conducted using MEGA ...
Appl. Comput. Math.
V.9, Special Issue, 2010, pp. 19-33
POSSIBLE FUNCTIONAL AND EVOLUTIONARY ROLE OF PLASTID DNA INSERTIONS IN RICE GENOME
YAGUT YU. AKBAROVA 1,2, VICTOR V. SOLOVYEV 3, ILHAM A. SHAHMURADOV 1
1 Bioinformatics Laboratory, Institute of Botany, Baku AZ1073, Azerbaijan
2 College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Sultanate of Oman
3 Department of Computer Science, Royal Holloway, University of London, Egham, Surrey TW20, UK
... of amino acid sequences has been carried out by BLAST program [1]. Search for statistically
significant open reading frames (ORFs) and putative target compartments of proteins were done
by BESTORF and ProtComp programs, respectively (http://www.softberry.com). ...
BMC Genomics.
2010 Jul 8;11:422
Comparative analysis of secreted protein evolution using expressed sequence tags from four poplar leaf rusts (Melampsora spp.)
Joly DL, Feau N, Tanguay P, Hamelin RC.
Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du PEPS, P,O, Box 10380, Stn, Sainte-Foy, Quebec, QC, G1V 4C7, Canada.
... gene models. Initial ORF prediction for Melampsora spp. was generated with the bestORF
algorithm (Softberry) using Ustilago parameters. Sequence analysis Similarity searches
for full length sequences and conserved domains were performed ...
Molecular Vision
2009; 15:2544-2553
Phenotypic characterisation and ZEB1 mutational analysis in posterior polymorphous corneal dystrophy in a New Zealand population
Vincent et al.,
1Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Medical and Health Science, University of Auckland, Auckland, New Zealand; 2Ophthalmology Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand
... Prediction of potential coding fragment in the reference mRNA (NM_0030751.4) sequence
containing the c.1A?G was performed using the BESTORF program (Softberry.Inc, Mount Kisco,
NY), and predicted translation initiation at nucleotide 788 which encodes the methionine ...
BMC Evolutionary Biology
2009, 9:97 doi:10.1186/1471-2148-9-97
Identification, distribution and molecular evolution of the pacifastin gene family in Metazoa
Bert Breugelmans, Gert Simonet, Vincent van Hoef, Sofie Van Soest, Jozef, Vanden Broeck
Department of Animal Physiology and Neurobiology, Zoological Institute, K.U.Leuven, Naamsestraat 59, B-3000 Leuven, Belgium
... presence of a signal peptide were predicted using BESTORF (http://www.softberry.com) and
SignalP (http://www.cbs.dtu.dk/services/SignalP/), respectively. ... If no complete ORF was found,
the Softberry splice finder tool (FSPLICE) was used to search the missing ...
FEBS Journal
Volume 275 Issue 6 Page 1103-1117, March 2008
Succinate dehydrogenase flavoprotein subunit expression in Saccharomyces cerevisiae– involvement of the mitochondrial FAD transporter, Flx1p
Teresa A. Giancaspero 1,
Robin Wait 2,
Eckhard Boles 3,
Maria Barile
1 Dipartimento di Biochimica e Biologia Molecolare "E. Quagliariello", Universita degli Studi di Bari, Italy
2 Kennedy Institute of Rheumatology Division, Faculty of Medicine, Imperial College London, UK
3 Institut fu"r Molekulare Biowissenschaften, J.W. Goethe-Universitat, Frankfurt am Main, Germany
... Both the NCBI tool orf finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html)
and the bestorf gene prediction program from Softberry Inc. ...
Microbiology
154 (2008), 1204-1217; DOI 10.1099/mic.0.2007/014944-0
Identification of soluble secreted proteins from appressoria of Colletotrichum higginsianum by analysis of expressed sequence tags
Jochen Kleemann, Hiroyuki Takahara, Kurt Stu"ber and Richard O'Connell
Max-Planck-Institute for Plant Breeding Research, Department of Plant–Microbe Interactions, D-50829 Koln, Germany
... different reading frame. BESTORF (Softberry) was used to confirm the ORF
of selected unique sequences. Proteins were considered ...
GENES & DEVELOPMENT
21:708-718, 2007
Ultraconserved elements are associated with homeostatic control of
splicing regulators by alternative splicing and nonsense-mediated decay
Julie Z. Ni et al.,
Center for Molecular Biology of RNA and Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
... Once the transcripts are predicted, an ORF finder (BESTORF from Softberry,
http://www.softberry.com) is used to find the best ORF. ...
Eukaryotic Cell, March 2005,
p. 526-535, Vol. 4, No. 3
Sex-Specific Homeodomain Proteins Sxi1 and Sxi2a Coordinately Regulate Sexual Development in Cryptococcus neoformans
Christina M. Hull,1, Marie-Josee Boily,1 and Joseph Heitman1,2*
Department of Molecular Genetics and Microbiology,1 the Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina2
... Sequence manipulations. Splice predictions of candidate gene sequences
for SXI2a
were facilitated with a Softberry algorithm (www.softberry.com). ...
...We utilized the BESTORF gene prediction algorithm
from Softberry, Inc., to electronically produce predicted spliced cDNA
products encoded by a 10-kb region....
Molecular and Cellular Endocrinology
Volume 348, Issue 1, 2 January 2012, Pages 313–321
Two novel mutations in the thyroglobulin gene as cause of congenital hypothyroidism: Identification a cryptic donor splice site in the exon 19
Hector M. Targovnik et al.,
a Laboratorio de Biologia Molecular, Catedra de Genetica y Biologia Molecular, Facultad de Farmacia y Bioquimica, Universidad de Buenos Aires, 1113 Buenos Aires, Argentina
b Unidad de Medicina Molecular, Departamento de Medicina, Facultad de Medicina, Universidad de Salamanca, 37007 Salamanca, Spain
c Service d’Endocrinologie Pediatrique, Hopital des Enfants, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse Cedex 9, France
... Searching for potential 5?ss sequences in the TG gene spanning exon 19 and intron 19 was
accomplished using the NNSplice (http://www.fruitfly.org/seq_tools/splice.html), Fsplice
(http://linux1.softberry.com/berry.phtml?topic=fsplice&group=programs&subgroup=gfind), SPL ...
Genome
2011, 54(12): 1041-1044, DOI: 10.1139/g11-068
Isolation of a strawberry gene fragment encoding an actin depolymerizing factor-like protein from genotypes resistant to Colletotrichum acutatum
Marta Ontivero, a Gustavo Martinez Zamor a,b Sergio Salazar, c Juan Carlos Diaz Ricci, b Atilio Pedro Castagnaro a
Seccion Biotecnologia, Estacion Experimental Agroindustrial Obispo Colombres-Unidad Asociada al INSIBIO, Av. William Cross 3150, 4101 Las Talitas, Tucuman, Argentina.
bInstituto Superior de Investigaciones Biologicas (INSIBIO; CONICET- UNT) and Instituto de Quimica Biologica “Dr. Bernabe Bloj”, Universidad Nacional de Tucuman. Chacabuco 461, 4000 Tucuman. Argentina.
... The deduced amino acid sequence showed identity scores ranging between 93% and 60%,
with E values comprised between 1 ? 10 –37 and 6 ? 10 –44 . The gene prediction programs
SPL and FGENESH 2.6 (www.softberry.com) (Solovyev et al. ...
J Med Genet
2010 47: 8-21 originally published online July 1, 2009 doi: 10.1136/jmg.2009.067249
Mutations in 3 genes (MKS3, CC2D2A and
RPGRIP1L) cause COACH syndrome (Joubert
syndrome with congenital hepatic fibrosis)
Doherty et al.,
1University of Washington,
Seattle, Washington, USA
2National Institutes of Health,
Bethesda, Maryland, USA
... the likelihood that missense mutations would be deleterious was made using the PolyPhen
program.42 NetGene2 (www.cbs.dtu.dk/services/NetGene2/), Genie (www.fruitfly.org/seq_tools/
splice.html), Human Splicing Finder (www.umd.be/HSF/), SPL (linux1.softberry.com), and ...
Molecular breeding
2010, vol. 25, no4, pp. 699-722
Development of SSR markers and construction of a consensus genetic map for chicory (Cichorium intybus L.)
Cadalen et al.,
1) GIS CARTOCHIC, USTL, 59655, Villeneuve d’Ascq, France
(2) UMR USTL/INRA 1281 «Stress Abiotiques et Differenciation des Vegetaux Cultives», ERT 1067, Universite de Lille 1, 59655, Villeneuve d’Ascq, France
... Intron positions were determined and then compared to predictions by models for intron/exon
boundaries determination with RNA SPL tool, http://www.softberry.com/berry.phtml or GeneMark
cDNA, http://opal.biology.gatech.edu/Gene Mark/genemark_cDNA_all.cgi. ...
J Med Genet
doi:10.1136/jmg.2009.067249
Mutations in 3 genes (MKS3, CC2D2A and RPGRIP1L) cause COACH syndrome (Joubert syndrome with congenital hepatic fibrosis)
Doherty et al.,
University of Washington, United States
... likelihood that missense mutations would be deleterious was made using the PolyPhen
program.[42] NetGene2 (www.cbs.dtu.dk/services/NetGene2/), Genie (www.fruitfly.org/seq_tools/
splice.html), Human Splicing Finder (www.umd.be/HSF/), SPL (linux1.softberry.com), and ...
European Journal of Human Genetics
12 Nov 2008, doi: 10.1038/ejhg.2008.21
Noncanonical and canonical splice sites: a novel mutation at the rare noncanonical splice-donor cut
site (IVS4+1A>G) of SEDL causes variable splicing isoforms in X-linked spondyloepiphyseal dysplasia tarda
Feng Xiong et al.,
1 Children's Hospital of Chongqing Medical University, Central District, Chongqing, PR China
2 Bio-X Center, Shanghai Jiao Tong University, Shanghai, China
...to search for cDNA and genomic DNA of SEDL-related splice variants.7 The FSPLICE
1.0 and SPL platforms (http://www.softberry.com/) were used to predict potential splice sites in genomic DNA. SPLM was implemented to substitute for SPL..
Blood Coagulation & Fibrinolysis.
19(3):240-242, April 2008.
Four novel FXI gene mutations in three factor XI- deficient patients
de Raucourt, Emmanuelle, de Mazancourt, Philippe, Quelin, Florence
Laboratory of Haematology, Poissy-Saint-Germain-en-Laye Hospital, France.
... exon 7, but an exon prediction software did not show an effect on the probability
of splicing (website: http://www.softberry.com/cgi-bin/programs/gfind/spl.pl ...
Annals of Human Genetics
Volume 71 Issue 3 Page 325-335, May 2006
Common Polymorphisms in the CACNA1H Gene Associated with
Childhood Absence Epilepsy in Chinese Han Population
J. Liang et al.,
Department of Pediatrics, Peking University, First Hospital, Beijing, 100034, P. R. China
... cmpharm.ucsf.edu/ ), transcription factor binding sites (NIH, http:/ /
thr.cit.nih.gov/ molbio/ ), potential splicing sites (SPL, http:/ / softberry.com/ ...
J. Biol. Chem.,
Vol. 281, Issue 40, 29753-29761, October 6, 2006
Regulation of Hypocretin (Orexin) Expression in Embryonic Zebrafish*
Juliette H. Faraco et al.,
Stanford University Center for Narcolepsy, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California 94305, the Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, and ¶INSERM, U784, 75230 Paris, France
... rate options. Fgenes, Fex, and Spl (Softberry.com) were used to identify
potential first exons and/or splice donor sites. Signal ...
The National Academy of Sciences
Proc Natl Acad Sci U S A.
2003 November 25; 100(Suppl 2): 14537-14542.
Molecular evolution of the insect chemoreceptor gene superfamily in Drosophila melanogaster
Hugh M. Robertson,* Coral G. Warr,and John R. Carlson
*Department of Entomology, University of Illinois, 505 South Goodwin Avenue, Urbana,
IL 61801; School of Biological Sciences, Monash University, Clayton VIC 3800, Australia;
and Department of Molecular, Cellular, and Developmental Biology, Yale University,
New Haven, CT 06520
The genes were reconstructed manually in the PAUP editor (23) by using the
expected exon/intron structures as guides and the SPL program (Softberry, www.softberry.com/berry.phtml) to locate predicted introns.
Hum. Mol. Genet.
(2012) 21 (16): 3647-3654. doi: 10.1093/hmg/dds194
Deep intronic mutation in OFD1, identified by targeted genomic next-generation sequencing, causes a severe form of X-linked retinitis pigmentosa (RP23)
Webb et al.,
1UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK,
2Jules Stein Eye Institute, University of California, 200 Stein Plaza, CA 90095-7000, USA
... SplicePredictor, http://deepc2.psi.iastate.edu/cgi-bin/sp.cgi. FSplice, http://linux1.softberry.
com/berry.phtml?topic=fsplice&group=programs&subgroup=gfind. SPLM, http://linux1.softberry.
com/berry.phtml?topic=splm&group=programs&subgroup=gfind. ...
European Journal of Human Genetics
12 Nov 2008, doi: 10.1038/ejhg.2008.21
Noncanonical and canonical splice sites: a novel mutation at the rare noncanonical splice-donor cut
site (IVS4+1A>G) of SEDL causes variable splicing isoforms in X-linked spondyloepiphyseal dysplasia tarda
Feng Xiong et al.,
1 Children's Hospital of Chongqing Medical University, Central District, Chongqing, PR China
2 Bio-X Center, Shanghai Jiao Tong University, Shanghai, China
... 7 The FSPLICE 1.0 and SPL platforms (http://www.softberry.com/) were used to predict
potential splice sites in genomic DNA. SPLM was implemented to substitute ...
Gene
Volume 594, Issue 1, 5 December 2016, Pages 131–137 http://dx.doi.org/10.1016/j.gene.2016.08.058
A novel exon generates ubiquitously expressed alternatively spliced new transcript of mouse Abcc4 gene
Vivian et al.,
Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
... Different online tools used in our study are GENSCAN (http://genes.mit.edu/GENSCAN.html),
FGENESH (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=
gfind), FEX (http://linux1.softberry.com/berry.phtml?topic=fex&group ...
Journal of plant physiology
2016, 195, 31-38. doi:10.1016/j.jplph.2016.03.004
In silico characterization of DNA motifs associated with the differential expression of the ornithine decarboxylase gene during in vitro cystocarp development in the red seaweed Grateloupia imbricata
Montero-Fernandez, M., Robaina, R. R., Garcia-Jimenez, P.
Departamento de Biologia, Facultad de Ciencias del Mar, Universidad of Las Palmas de Gran Canaria, E-35017 Las Palmas de Gran Canaria, Canary Islands, Spain
... FEX: http://linux1.softberry.com/berry.phtml?topic=fex&group=
programs&subgroup=gfind, Finding potential 5?-, internal and 3'-coding exons. ...
IUBMB Life
2015, Volume 68, Issue 2, pages 122–135, February 2016 DOI: 10.1002/iub.1464
Identification of differentially expressed three novel transcript variants of mouse ARNT gene
Ishqi, H. M., Ur Rehman, S., Sarwar, T., Husain, M. A., Tabish, M.
Institute
... finding tools. Gene finding tools used in our study were HMM gene (http://www.cbs.
dtu.dk/services/HMMgene/), Genebuilder (http://www.itba.mi.cnr.it/webgene/) and
FGENESH (http://linux1.softberry.com/berry.phtml). "Fex" available ...
International Journal of Bioinformatics Research and Applications
Volume 9, Number 6/2013, pp. 557-575 DOI: 10.1504/IJBRA.2013.056630
In–silico analysis for RNA–interference mechanism of a–synuclein to treat Parkinson's disease
S. Seema 1, R. Seenivasagam 2, K. Hemavathi 3
1Department of Bioinformatics, University of East London, Docklands Campus, University Way, London E16 2RD, UK
2Division of Drug Discovery and Development, Center of Molecular and Computational Biology, Department of Botany, St. Joseph's College, P.B. 27094, 36, Langford Road, Bangalore, Karnataka 560027, India
3Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur - 613 402, Tamil Nadu, India
... 2009). The FEX program (Find EXon) (http://www.softberry.com/berry.phtml) predicts
internal exons by linear discriminate function, evaluating ORFs flanked by GT and
AG base pairs (the 5? and 3? ends of typical introns). ...
Plant Molecular Biology Reporter
April 2013, Volume 31, Issue 2, pp 303-313, DOI: 10.1007/s11105-012-0499-2
Molecular characterization of a cellulose synthase gene (AaxmCesA1) isolated from an Acacia auriculiformis x Acacia mangium hybrid
Seok Yien Christina Yong 1 and Ratnam Wickneswari 2
(1)Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
(2)School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia
... cgi /iprscan.cgi). Promoter sequence was analyzed using Prediction of Plant Promoter
(http:// www.softberry.com/berry.phtml) and Neural Network Pre- diction
(http://www.fruitly.org/seq_tools/promoter.html) software. The cDNA ...
The software “Finding 5?, internal and 3? coding exons”
(http://linux.softberry.com/cgi-bin/progrmas/gfind/fex.pl) was applied to predict exon–intron boundaries.
Cell Biology International.
(2013), doi: 10.1002/cbin.10080
Computational prediction and characterisation of ubiquitously expressed new splice variant of Prkaca gene in mouse.
Banday, A. R., Azim, S., Hussain, M. A., Nehar, S. and Tabish, M.
1Faculty of Life Sciences, Department of Biochemistry, A.M. University, Aligarh, Uttar Pradesh, India
2P.G. Department of Zoology, Ranchi University, Ranchi, Jharkhand, India
... (http://cbcb.umd.edu/software/GeneSplicer/) (Pertea et al., 2001), FGENESH (http://www.softberry.
com/berry.phtml) and FEX (http://www.softberry.com/berry.phtml) and Augustus (http://augustus.
gobics.de/) (Stanke et al., 2004). Alignment analysis was carried out using ...
Molecular Immunology
Volume 46, Issues 8-9, May 2009, Pages 1679-1687
The immunoglobulin heavy chain locus in the reptile Anolis carolinensis
Francisco Gambon Deza, Christian Sanchez Espinel and Susana Magadan Mompo
aUnidad de Inmunologia, Hospital do Meixoeiro, Carretera de Madrid s/n°, Vigo 36210, Pontevedra, Spain
bInstituto Superior de Saude do Alto Ave (ISAVE), Quinta de Matos, Geraz do Minho, 4830-31 PVL, Portugal
... The constant region genes and exons were obtained by comparison with those already described
for E. macularius. A dotplot was made with E. macularius and A. carolinensis sequences using
the DNASTAR (lasergene), FGENESH and FEX software (http://www.softberry.com). ...
Fungal Genetics and Biology
Volume 44, Issue 5, May 2007, Pages 415-429
Mating-type genes and the genetic structure of a world-wide collection of the tomato pathogen Cladosporium fulvum
Ioannis Stergiopoulos et al.,
Laboratory of Phytopathology, Wageningen University and Research Centre, Binnenhaven 5, 6709 PD Wageningen, The Netherlands
... Barcelona, Spain) and the FEX (Solovyev et al., 1994) and FGENESH (Salamov and Solovyev,
2000) programs from the MOLQUEST software package (Softberry Inc. ...
J. Biol. Chem.,
Vol. 281, Issue 40, 29753-29761, October 6, 2006
Regulation of Hypocretin (Orexin) Expression in Embryonic Zebrafish*
Juliette H. Faraco et al.,
Stanford University Center for Narcolepsy, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California 94305, the Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, and ¶INSERM, U784, 75230 Paris, France
... rate options. Fgenes, Fex, and Spl (Softberry.com) were used to identify
potential first exons and/or splice donor sites. Signal ...
The Journal of Immunology,
2006, 176: 4221-4234.
Complete Sequence Assembly and Characterization of the C57BL/6 Mouse Ig Heavy Chain V Region
Colette M. Johnston2, Andrew L. Wood, Daniel J. Bolland and Anne E. Corcoran3
Laboratory of Chromatin and Gene Expression, Babraham Institute, Babraham Research Campus, Cambridge CB2 4AT, United Kingdom
... and databases, thereby providing optimal consensus for gene predictions: GRAIL (
http://compblo.ornl.gov/Grail-1.3/ ), Fex ( http://www.softberry.com ), Hexon ...
Biochemical and Biophysical Research Communications
Volume 313, Issue 3, 16 January 2004, Pages 765-770
p73: in silico evidence for a putative third promoter region
A.Emre Sayana, Mario Rossia, Gerry Melinoa, b and Richard A Knight
Medical Research Council Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
... exons in these introns. Three out of six programs are the part of Softberry
package [24] having different algorithms. FEX is looking ...
Current Biology
2004, Volume 14, Issue 19, Pages R832-R833
Dual capacity of a human olfactory receptor
M. Spehr, K. Schwane, S. Heilmann, G. Gisselmann, T. Hummel, H. Hatt
... (B) RT-PCR with intron spanning primers. Candidates for 5'UTR exons were identified
using FGENES and FEX software (SoftBerry, Mount Kisco, NY). ...
BMC Genomics
2011, 12:110 doi:10.1186/1471-2164-12-110
Strain-specific copy number variation in the intelectin locus on the 129 mouse chromosome 1
Lu et al.,
The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Roslin, Midlothian, UK
... Pseudogenes were only annotated when their exons share at least 70% identity to the coding
sequences. In addition, the exon-exon junctions of the predicted transcripts were predicted with
the RNASPL program of the Softberry web server [61] to check for alternative splicing. ...
General and Comparative Endocrinology
Volume 169, Issue 3, 1 December 2010, Pages 192-196 doi:10.1016/j.ygcen.2010.09.014
Molecular cloning and characterization of preproorexin in winter skate (Leucoraja ocellata)
Erin E. MacDonald and Helene Volkoff
a Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada A1B 3X9
b Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL, Canada A1B 3X9
... Possible exon-exon locations were predicted using RNASPL (Softberry.com) and the most
probable location was chosen based on the location of intron in known fish species (Faraco et
al., 2006) and the fact that (A/C)AG is the most common exon sequence at the donor site ...
Scientific Reports
2017;7: 40416. doi: 10.1038/srep40416
Immunoglobulin light chain (IGL) genes in torafugu: Genomic organization and identification of a third teleost IGL isotype
Fu X, Zhang F, Watabe S, Asakawa S.
1State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
2Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
3School of Marine Bioscience, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
... Splice sites between leader and V exons were discerned by FSPLICE (http://linux1.softberry.com/
berry.phtml). Exon boundaries of V L , J L , and C L were refined by alignment with known
VJ-C cDNA sequences and torafugu EST sequences (from Fugu Genome Project) 38 . ...
Molecular and cellular endocrinology
2016, 419, 172-184. doi:10.1016/j.mce.2015.10.014
Compound heterozygous DUOX2 gene mutations (c. 2335-1G> C/c. 3264_3267delCAGC) associated with congenital hypothyroidism. Characterization of complex cryptic splice sites by minigene analysis
Belforte, F. S. et al.,
a Laboratorio de Genetica Molecular Tiroidea, Instituto de Inmunologia, Genetica y Metabolismo (INIGEM, CONICET-UBA), Hospital de Clinicas “Jose de San Martin”, C1120AAR Buenos Aires, Argentina
b Laboratorio de Genetica y Biologia Molecular, Instituto de Inmunologia, Genetica y Metabolismo (INIGEM, CONICET-UBA), Hospital de Clinicas “Jose de San Martin”, C1120AAR Buenos Aires, Argentina
... Searching for potential 5? ss and 3? ss sequences in the DUOX2 gene spanning from intron
17 to intron 18 was accomplished using the NNSplice (http://www.fruitfly.org/seq_tools/splice.
html), Fsplice (http://linux1.softberry.com/berry.phtml?topic=fsplice&group ...
Journal of Cell and Tissue Research
2015, 15(3), 5181-5186.
CLONING AND EXPRESSION OF PLANT CODON OPTIMIZED CRY1AC GENE IN SACCHAROMYCES CEREVISIAE
Mohan, T. C. et al.,
... Splice sites were predicted by using softberry FSPLICE (Find Splice Site in Genomic DNA) option
accessible through http://www.softberry.com. The sequence was analyzed for undesirable 5'
mRNA secondary structure by using tools available at http//www. genebee.com. ...
Journal of Cell & Tissue Research
Dec2015, Vol. 15 Issue 3, p5181-5186. 6p.
CLONING AND EXPRESSION OF PLANT CODON OPTIMIZED CRY1AC GENE IN SACCHAROMYCES CEREVISIAE
MOHAN, T. C.; KUMARA SWAMY, G. K.; KRISHNARAJ, P. U.; MISRA, H. S.; KURUVINASHETTI, M. S.
... Splice sites were predicted by using softberry FSPLICE (Find Splice Site in Genomic DNA) option
accessible through http://www.softberry.com. The sequence was analyzed for undesirable 5'
mRNA secondary structure by using tools available at http//www. genebee.com. ...
Molecular and cellular endocrinology
2015, 404, 102-112. doi:10.1016/j.mce.2015.01.032
Novel compound heterozygous Thyroglobulin mutations c. 745+ 1G> A/c. 7036+ 2T> A associated with congenital goiter and hypothyroidism in a Vietnamese family. Identification of a new cryptic 5? splice site in the exon 6
Citterio et al.,
a Laboratorio de Genetica y Biologia Molecular, Instituto de Inmunologia, Genetica y Metabolismo (INIGEM, CONICET-UBA), Hospital de Clinicas “Jose de San Martin”, C1120AAR Buenos Aires, Argentina
b Catedra de Genetica y Biologia Molecular (FFyB-UBA), C1113AAD Buenos Aires, Argentina
c Unite Endocrinologie Diabetologie Pediatrique and Centre des Maladies Rares de la Receptivite Hormonale, CHU-Angers, 49933 Angers CEDEX 9, France
... Searching for potential 5? ss sequences in the TG gene spanning from exon 6 to intron 6 and exon
40 to intron 40 was accomplished using the NNSplice (http://www.fruitfly.org/seq_tools/splice.html),
Fsplice (http://linux1.softberry.com/berry.phtml?topic=fsplice&group ...
ISRN Computational Biology
Volume 2013 (2013), Article ID 790240, 6 pages http://dx.doi.org/10.1155/2013/790240
Zebra Finch Glucokinase Containing Two Homologous Halves Is an In Silico Chimera
Khrustalev Vladislav Victorovich, 1 Lelevich Sergey Vladimirovich, 2 and Barkovsky Eugene Victorovich 1
1Department of General Chemistry, Belarusian State Medical University, Dzerzinskogo 83, 220116 Minsk, Belarus
2Department of Clinical Laboratory Diagnostics, Allergology and Immunology, Grodno State Medical University, Gorkogo 80, 230009 Grodno, Belarus
... Levels of 1GC; 2GC and 3GC have been calculated by “VVK Protective Buffer” [5] in those
newly described exons too. Splicing sites for “new” exons have been predicted by "FSPLICE"
algorithm from SoftBerry server (http://linux1.softberry.com/). ...
BMC Genomics
2013, 14:34 doi:10.1186/1471-2164-14-34
Developmentally regulated expression and complex processing of barley pri-microRNAs
Kruszka et al.,
1 Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
2 Computational Genomics Laboratory - Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
...Intron positions were predicted by comparisons of genomic and cDNA sequences using FSPLICE software, http://linux1.softberry.com webcite[53]. ...
Hum. Mol. Genet.
(2012) 21 (16): 3647-3654. doi: 10.1093/hmg/dds194
Deep intronic mutation in OFD1, identified by targeted genomic next-generation sequencing, causes a severe form of X-linked retinitis pigmentosa (RP23)
Webb et al.,
1UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK,
2Jules Stein Eye Institute, University of California, 200 Stein Plaza, CA 90095-7000, USA
... SplicePredictor, http://deepc2.psi.iastate.edu/cgi-bin/sp.cgi. FSplice, http://linux1.softberry.
com/berry.phtml?topic=fsplice&group=programs&subgroup=gfind. SPLM, http://linux1.softberry.
com/berry.phtml?topic=splm&group=programs&subgroup=gfind. ...
Journal of the Peripheral Nervous System
Volume 17, Issue 2, pages 141–146, June 2012 DOI: 10.1111/j.1529-8027.2012.00405.x
Two novel missense mutations in FGD4/FRABIN cause Charcot-Marie-Tooth type 4H (CMT4H)
Baudot et al.,
1Inserm, UMR 910, “Genetique Medicale et Genomique Fonctionnelle”, Faculte de Medecine de la Timone
2Aix-Marseille Univ, UMR 910, “Genetique Medicale et Genomique Fonctionnelle”, Faculte de Medecine de la Timone, Marseille, France
... variations on splicing was assessed using the following programs: ESE finder (http://rulai.cshl.
edu/cgi-bin/tools/ESE3/esefinder.cgi?process=home), NNSplice (http://biologyhelp.awardspace.
com/desc.php?id=147&type=biotech), and FSPLICE (http://linux1.softberry.com/berry ...
Breast Cancer Research and Treatment
April 2012, Volume 132, Issue 3, pp 979-992 DOI
10.1007/s10549-011-1661-5
Assessing the RNA effect of 26 DNA variants in the BRCA1 and BRCA2 genes
Mireia Menendez et al.,
1. Hereditary Cancer Program, Genetic Diagnosis Unit, Laboratori de Recerca Translacional, Institut Catala d’Oncologia, Hospital Duran i Reynals—Bellvitge Biomedical Research Institute (ICO-IDIBELL), L’Hospitalet de Llobregat, Barcelona and Hospital Josep Trueta, IDIBGI, Gran Via 199-203, Girona, 08908, Spain
2. Human Cancer Genetics, Spanish National Cancer Centre (CNIO), Madrid, Spain
... www.fruitfly.org/seq_tools/splice. html), NetGene2 Server (http://www.cbs.dtu.dk/
services/ NetGene2/) and SoftBerry (http://linux1.softberry.com/berry. phtml?topic=
fsplice&group=programs&subgroup=gfind). In the case of intronic ...
Molecular and Cellular Endocrinology
Volume 348, Issue 1, 2 January 2012, Pages 313–321
Two novel mutations in the thyroglobulin gene as cause of congenital hypothyroidism: Identification a cryptic donor splice site in the exon 19
Hector M. Targovnik et al.,
a Laboratorio de Biologia Molecular, Catedra de Genetica y Biologia Molecular, Facultad de Farmacia y Bioquimica, Universidad de Buenos Aires, 1113 Buenos Aires, Argentina
b Unidad de Medicina Molecular, Departamento de Medicina, Facultad de Medicina, Universidad de Salamanca, 37007 Salamanca, Spain
c Service d’Endocrinologie Pediatrique, Hopital des Enfants, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse Cedex 9, France
... Searching for potential 5?ss sequences in the TG gene spanning exon 19 and intron 19 was
accomplished using the NNSplice (http://www.fruitfly.org/seq_tools/splice.html), Fsplice
(http://linux1.softberry.com/berry.phtml?topic=fsplice&group=programs&subgroup=gfind), SPL ...
Aging Cell
(2011), 10: 896–907. doi: 10.1111/j.1474-9726.2011.00727.x
Alternative splicing factor or splicing factor-2 plays a key role in intron retention of the endoglin gene during endothelial senescence.
Blanco, F. J. and Bernabeu, C.
Centro de Investigaciones Biologicas, Consejo Superior de Investigaciones Cientificas (CSIC), and Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), c/Ramiro de Maeztu 9, 28040 Madrid, Spain
... Genome Bioinformatics (http://genome.ucsc.edu/). Then, the FSPLICE and FGENESH
tools were used to predict exons and introns in the DNA sequences (http://linux1.
softberry.com/berry.phtml). The Transeq tool at the European ...
Clinical Gastroenterology and Hepatology
Volume 9, Issue 9 , Page 806, September 2011 DOI: 10.1016/j.cgh.2011.03.034
Lynch Syndrome in Young-Onset Colorectal Cancer: Reassessing the Role of the MSH6 Gene
Maria Dolores Giraldez, Antoni Castells, Sergi Castellvi-Bel
Department of Gastroenterology, Hospital Clinic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Spain
... By applying our strategy to the Limburg study (PolyPhen [http://genetics.bwh.harvard.edu/pph/],
NNSPLICE [http://www.fruitfly.org/seq_tools/splice.html], and FSPLICE [http://linux1.softberry.
com/berry.phtml?topic=fsplice&group=programs&subgroup=gfind]), 8 of their patients ...
Phytopathologia Mediterranea
49, jan. 2011.
Amplification of Polyketide Synthase gene fragments in ochratoxigenic and nonochratoxigenic black aspergilli in grapevine.
STORARI, M., PERTOT, I., GESSLER, C., BROGGINI, G.
... Arbor, MI, USA). Putative introns were deter- mined using FSplice (www.softberry.
com) and by homology with similar PKSs found in the NCBI database using BLASTX
(http://blast.ncbi.nlm. nih.gov/Blast.cgi). Deduced amino ...
Chem. Senses
(2011) 36 (2): 149-160. doi: 10.1093/chemse/bjq105
Conservation of Indole Responsive Odorant Receptors in Mosquitoes Reveals an Ancient Olfactory Trait
Bohbot et al.,
1Departments of Biological Sciences and Pharmacology, Center for Molecular Neuroscience, Institutes of Chemical Biology and Global Health and Program in Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37235, USA
2Henry A. Wallace Beltsville Agricultural Research Center, Plant Sciences Institute, Invasive Insect Biocontrol and Behavior Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
... Home.html). Matches were manually annotated using ClustalW and refined using
the Softberry Splice Site Prediction program (http://linux1.softberry.com/berry.phtml?
topic=fsplice&group=programs&subgroup=gfind). ClustalW ...
Microbiology
156 (2010), 2549-2557; DOI 10.1099/mic.0.039735-0
Molecular characterization and expression analysis of a suite of cytochrome P450 enzymes implicated in insect hydrocarbon degradation in the entomopathogenic fungus Beauveria bassiana
Nicolas Pedrini 1,2, Shizhu Zhang 1, M. Patricia Juarez 2 and Nemat O. Keyhani 1
1 Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
2 Instituto de Investigaciones Bioquimicas de La Plata, CONICET, Facultad de Ciencias Medicas, UNLP, Calles 60 y 120 (1900), La Plata, Argentina
... Sequence analyses. The sequences were analysed using programs implemented at the Biology
WorkBench website (http://workbench.sdsc.edu/); splice site analysis was performed using the
FSPLICE program at the SoftBerry server (http://www.softberry.com/berry.phtml). ...
Neurology
2010 Feb 2;74(5):366-71
Genetic contribution of FUS to frontotemporal lobar degeneration
Van Langenhove et al.,
Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, University of Antwerp-CDE, Universiteitsplein 1, B-2610 Antwerpen, Belgium.
.. the protein. The effect of sequence variants on splice site function and the prediction
of alternative splice sites were assessed by the programs FSPLICE (http://www.
softberry.com), NetGene2, 27 and NNSplice. 28. RESULTS. ...
Chem. Senses
2010, doi: 10.1093/chemse/bjq105
Conservation of Indole Responsive Odorant Receptors in Mosquitoes Reveals an Ancient Olfactory Trait
Bohbot et al.,
1 Departments of Biological Sciences and Pharmacology, Center for Molecular Neuroscience, Institutes of Chemical Biology and Global Health and Program in Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37235, USA
2 Henry A. Wallace Beltsville Agricultural Research Center, Plant Sciences Institute, Invasive Insect Biocontrol and Behavior Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
... Home.html). Matches were manually annotated using ClustalW and refined using
the Softberry Splice Site Prediction program (http://linux1.softberry.com/berry.phtml?
topic=fsplice&group=programs&subgroup=gfind). ClustalW ...
Neurology.
2010 Mar 9;74(10):846-50.
THAP1 mutations (DYT6) are an additional cause of early-onset dystonia
Houlden et al.,
From the Department of Molecular Neuroscience (H.H., R.P., A.M., J.H.), Sobell Department of Motor Neuroscience and Movement Disorders (S.A.S., P.S., M.E., K.P.B.), University College London Institute of Neurology, England;
... This intronic change is unlikely to be pathogenic because it did not affect splicing using the
SpliceView program (http://bioinfo.itb.cnr.it/oriel/splice-view.html), NNSPLICE 0.9
(http://www.fruitfly.org/seq_tools/splice.html), and FSPLICE 1.0 (http://linux1.softberry.com/berry. ...
Eur J Hum Genet.
2011 Jan;19(1):56-63. Epub 2010 Aug 18
Characterization of novel SLC6A8 variants with the use of splice-site analysis tools and implementation of a newly developed LOVD database
Betsalel et al.,
Metabolic Unit, Department of Clinical Chemistry, VU University Medical Center, Amsterdam, The Netherlands.
... Project 6 (http://www.fruitfly.org/seq_tools/splice.html), Netgene2 7 (http://www.cbs.dtu.dk/services/
NetGene2/), Splice Predictor 8 (http://deepc2.psi.iastate.edu/cgi-bin/sp.cgi), GenscanW 9
(http://genes.mit.edu/GENSCAN.html) and FSplice (http://linux1.softberry.com/berry.phtml ...
Hum. Mol. Genet.
2010 19 (21): 4201-4206. doi: 10.1093/hmg/ddq338
A novel SOD1 splice site mutation associated with familial ALS revealed by SOD activity analysis
Birve et al.,
1Department of Pharmacology and Clinical Neuroscience and
2Department of Medical Biosciences, Clinical Chemistry, Umea University, Umea, Sweden
... The analyses of mRNA (Fig. 1B), fibroblast extracts (Fig. 2A) and erythrocytes (Fig. 2B) combine
to show that the usage of the alternative splice site must be close to complete for the mutant allele,
which was only predicted by the program FSPLICE at www.softberry.com. ...
BMC Evolutionary Biology
2009, 9:97 doi:10.1186/1471-2148-9-97
Identification, distribution and molecular evolution of the pacifastin gene family in Metazoa
Bert Breugelmans, Gert Simonet, Vincent van Hoef, Sofie Van Soest, Jozef, Vanden Broeck
Department of Animal Physiology and Neurobiology, Zoological Institute, K.U.Leuven, Naamsestraat 59, B-3000 Leuven, Belgium
... presence of a signal peptide were predicted using BESTORF (http://www.softberry.com) and
SignalP (http://www.cbs.dtu.dk/services/SignalP/), respectively. ... If no complete ORF was found,
the Softberry splice finder tool (FSPLICE) was used to search the missing ...
PLoS ONE.
2009; 4(2): e4372.
Identification of Lympho-Epithelial Kazal-Type Inhibitor 2 in Human Skin as a Kallikrein-Related Peptidase 5-Specific Protease Inhibitor
Ulf Meyer-Hoffert, Zhihong Wu, and Jens-Michael Schroder
Department of Dermatology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
... Subsequent sequence manipulations utilized the online BLAST 2 Sequences [37]
(http://www.ncbi.nlm.nih.gov/ blast/bl2seq/bl2.html). Splice site analysis was performed using
the FSPLICE program implemented at the SoftBerry server (http://www.softberry.com/berry.phtml). ...
Fungal Genetics and Biology
Volume 46, Issue 1, Supplement 1, March 2009, Pages S14-S18
Analysis and prediction of gene splice sites in four Aspergillus genomes
Kai Wang, David Wayne Ussery and Soren Brunak
aCenter for Biological Sequence Analysis, Department of Systems Biology, Building 208, Technical University of Denmark, DK-2800 Lyngby, Denmark
... 1407 donor sites), and most of them are likely to be false positives (Table 3). On
the other hand, FSPLICE predicts splice sites based on weight matrices model on
many organisms including Aspergillus (www.softberry.com). ...
PLoS ONE.
2009; 4(4): e5227.
Molecular Identification and Expression Analysis of Filaggrin-2, a Member of the S100 Fused-Type Protein Family
Zhihong Wu, Britta Hansmann, Ulf Meyer-Hoffert, Regine Glaser, and Jens-Michael Schroder
Department of Dermatology, University Hospital of Schleswig-Holstein, Kiel, Germany
... Subsequent sequence manipulations utilized the online BLAST 2 Sequences [62]
(http://www.ncbi.nlm.nih.gov/ blast/bl2seq/bl2.html). Splice site analysis was performed using
the FSPLICE program implemented at the SoftBerry server (http://www.softberry.com/berry.phtml). ...
European Journal of Human Genetics
12 Nov 2008, doi: 10.1038/ejhg.2008.21
Noncanonical and canonical splice sites: a novel mutation at the rare noncanonical splice-donor cut
site (IVS4+1A>G) of SEDL causes variable splicing isoforms in X-linked spondyloepiphyseal dysplasia tarda
Feng Xiong et al.,
1 Children's Hospital of Chongqing Medical University, Central District, Chongqing, PR China
2 Bio-X Center, Shanghai Jiao Tong University, Shanghai, China
...to search for cDNA and genomic DNA of SEDL-related splice variants.7 The FSPLICE 1.0 and SPL platforms (http://www.softberry.com/) were used to predict potential splice sites in genomic DNA. SPLM was implemented to substitute for SPL..
Genetics
Vol. 176, 749-761, June 2007
The Centromeric Retrotransposons of Rice Are Transcribed and Differentially Processed by RNA Interference
Pavel Neumann, Huihuang Yan and Jiming Jiang
Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
... Splice site analysis was performed using the FSPLICE program implemented at
the SoftBerry server (http://www.softberry.com/berry.phtml). ...
Journal of Biochemistry and Molecular Biology
Vol. 40, No. 2, March 2007, pp. 172-179
PCR-mediated Recombination of the Amplification Products of the Hibiscus
tiliaceus Cytosolic Glyceraldehyde-3-phosphate Dehydrogenase Gene
Linghui Wu, Tian Tang, Renchao Zhou and Suhua Shi*
State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education,
School of Life Sciences, Sun Yat-Sen University, 510275 Guangzhou, China
...The boundaries of exons/introns
in the obtained sequences were determined using FSPLICE
(Softberry Inc.) combined with BLAST (blastn, tblastx and bl2seq)
(Altschul et al., 1997; Tatusova and Madden, 1999).
...
The American Journal of Human Genetics
2005, Volume 76, Issue 5, Pages 729-749
Diversity and Function of Mutations in P450 Oxidoreductase in Patients with Antley-Bixler Syndrome and Disordered Steroidogenesis
Huang et al.,
... and "Frame 7" (table 4), disrupted the canonical splice-acceptor or -donor sites;
the splice-site recognition programs FSPLICE (see the Softberry Web site ...
Nature
425, 209-215 (11 September 2003) | doi:10.1038/425209a
Bioinformatics: Programmed for success
Steve Buckingham
... Three-way synteny from Softberry. Fast searching is also a
feature of Genome Explorer
from Softberry in Mount Kisco, New York, which uses the FMAP algorithm. ...
...... Softberry, for example, offers a number of gene-prediction programs that can be accessed over
the web, including FGENESH, which ... The fully automated FGENESH++C will automatically
annotate any genome (other than human) to a standard claimed to be indistinguishable ...
International Journal of Evolutionary Biology
Volume 2013 (2013), Article ID 818954, 10 pages
http://dx.doi.org/10.1155/2013/818954
Conservation/Mutation in the Splice Sites of Cytokine Receptor Genes of Mouse and Human
Rosa Calvello, Antonia Cianciulli, and Maria Antonietta Panaro
Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70126 Bari, Italy
... invertebrates, fungi, protozoa, and plants [25–30]. Comprehensive databases have
also been generated, for example, http://www.softberry.com/spldb/SpliceDB.html
[29–31], and [26]. Cumulatively, the above-quoted papers report ...
European Journal of Human Genetics
12 Nov 2008, doi: 10.1038/ejhg.2008.21
Noncanonical and canonical splice sites: a novel mutation at the rare noncanonical splice-donor cut
site (IVS4+1A>G) of SEDL causes variable splicing isoforms in X-linked spondyloepiphyseal dysplasia tarda
Feng Xiong et al.,
1 Children's Hospital of Chongqing Medical University, Central District, Chongqing, PR China
2 Bio-X Center, Shanghai Jiao Tong University, Shanghai, China
... 9 Exons 3, 4, 5 and 6 (containing the ... canonical and noncanonical mammalian splice
sites (SpliceDB) was used ... and SPL platforms (http://www.softberry.com/) were ...
JOURNAL OF COMPUTATIONAL BIOLOGY
Volume 12, Number 6, 2005 Pp. 894-906
Finding short DNA motifs using permuted markov models
X Zhao, H Huang, TP Speed
... The data are human donor sequences from SpliceDB[9], a recently developed database
of known mammalian splice site sequences (http://www.softberry.com/spldb ...
Current Opinion in Structural Biology
2004, 14:273-282
The evolving roles of alternative splicing
Liana F Lareau1, Richard E Green1, Rajiv S Bhatnagar2,3 and Steven E Brenner1,2_
Departments of 1Molecular and Cell Biology, and 2Plant and Microbial
Biology, University of California, Berkeley, California 94720, USA
3Department of Dermatology, University of California, San Francisco,
California 94143, USA
... [79] SpliceDBhttp://www.softberry.com/berry.phtml?topic?SpliceDBDatabase and
composition statistics for mammalian splice sites inferred from ESTs [80] ...
Yearbook of Medical Informatics.
Review Paper. 2004 121-136
Curated databases and their role in clinical bioinformatics
CC Englbrecht, M Han, MT Mader, A Osanger KFX Mayer
MIPS, Institute for Bioinformatics
...SpliceDB
http://www.softberry.com/spldb/SpliceDB.html
Canonical and non-canonical mammalian splice sites [122]
122.Burset M, Seledtsov IA, Solovyev VV. SpliceDB: database of canonical and non-canonical mammalian splice sites. Nucleic Acids Res 2001;29:255-9
Nucleic Acids Research,
2001, Vol. 29, No. 1 255-259
SpliceDB: database of canonical and non-canonical mammalian splice sites
M. Burset, I. A. Seledtsov1 and V. V. Solovyev*
The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK and 1Softberry Inc., 108 Corporate Park Drive, Suite 120, White Plains, NY 10604, USA
Theoretical and Applied Genetics
2016, 129(2), 305-316. DOI: 10.1007/s00122-015-2628-4
Identification and mapping of Tril, a homeodomain-leucine zipper gene involved in multicellular trichome initiation in Cucumis sativus
Wang, Y. L. et al.,
1. School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
2. Hunan Vegetable Research Institute, Hunan Academy of Agriculture Sciences, Changsha, 410125, China
... The functions of candi- date genes were retrieved from the NCBI website (http:// archive-dtd.ncbi.
nlm.nih.gov/). According to dicot plant (Arabidopsis)-based gene structure prediction (http://
linux1.softberry.com/), the Cucsa.045360 gene structure was identified in the tril mutant. ...
Proceedings of the National Academy of Sciences, India Section B: Biological Sciences,
2014, 84(1), 131-143. DOI:
Organization and classification of cytochrome P450 genes in Castor (Ricinus communis L.).
Kumar, M. S., Babu, P. R., Rao, K. V., & Reddy, V. D.
1. Centre for Plant Molecular Biology, Osmania University, Hyderabad, 500007, India
... The CYP proteins which are below 300 and above 600 amino acids were validated
by using Softberry gene prediction tool (http://linux1.softberry. com/berry.phtml) by
increasing the scaffold size to 2,000 bp upstream of 50 end. ...
Plant Systematics and Evolution
2014, 1-6. DOI: 10.1007/s00606-014-1066-0
Classification of cytochrome P450s in common bean (Phaseolus vulgaris L.)
Kumar, M. S., Chakravarthy, S. S., Babu, P. R., Rao, K. V., & Reddy, V. D.
1. Centre for Plant Molecular Biology, Osmania University, Hyderabad, 500 007, India
... The CYP proteins which are below 300 and above 600 amino acids were validated
using Soft- berry gene prediction tool (http://linux1.softberry.com/ berry.phtml) by
increasing the scaffold size to 2,000 bp upstream of 50 end. ...
Tree Genetics &: Genomes
2014, 10(2), 399-409. DOI: 10.1007/s11295-013-0695-8
Structural organization, classification and phylogenetic relationship of cytochrome P450 genes in Citrus clementina and Citrus sinensis
Mittapelli, S. R., Maryada, S. K., Khareedu, V. R., & Vudem, D. R.
1. Centre for Plant Molecular Biology, Osmania University, Hyderabad, 500 007, India
... Out-of- range CYP candidate proteins which are below 300 and above 600 amino acids
were validated by using Softberry gene prediction tool (http://linux1.softberry.com/berry.phtml)
by increasing the scaffold size to 2,000-bp upstream of 5? end. ...
Journal of Molecular Catalysis B: Enzymatic, 104, 23-28.
2014, 104, 23-28. DOI: 10.1016/j.molcatb.2014.03.001
Characterization of a novel cold-adapted phosphinothricin N-acetyltransferase from the marine bacterium Rhodococcus sp. strain YM12.
Wu G. et al.,
a State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
b Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, College of Life Science, Tarim University, Alar 843300, Xinjiang, China
... 2.4. Gene analysis and cloning. DNA sequences were analyzed using the Softberry Gene Finding
tool (http://linuxl.softberry.com/berry/). The DNA and protein sequence alignments were carried
out using the Blast program (http://blast.ncbi.nlm.nih.gov/Blast). ...
Enzyme and Microbial Technology.
Volume 63, September 2014, Pages 64–70 DOI: 10.1016/j.enzmictec.2014.02.010
Characterization and site-directed mutagenesis of a novel class II 5-enopyruvylshikimate-3-phosphate (EPSP) synthase from the deep-sea bacterium Alcanivorax sp L27
Zhang Y. et al.,
a State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
b National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
... 2.4. Gene Analysis. The recombinant plasmid pUC-3.66k was sequenced by
Genscript. (Nanjing, China), and the nucleotide sequences were analyzed using
the Softberry Gene Finding tool (http://linuxl.softberry.com/berry/). ...
Microbiology
2014, mic.0.077818-0 DOI: 10.1099/mic.0.077818-0
Calcineurin phosphatase and phospholipase C are required for developmental and pathological functions in the citrus fungal pathogen Alternaria alternata.
Tsai H. C., Chung K. R.
Institute of Food and Agricultural Sciences, University of Florida, USA
... Open reading 23 Page 8. Microbiology 8 frame (ORF) and exon/intron positions were
predicted using Softberry gene-finding software 1 (http://www.softberry.com). Fungal
RNA was purified with Trizol reagent (Molecular Research 2 ...