PloS one
2017 Feb 3;12(2):e0171410. doi:10.1371/journal.pone.0171410
Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks
Umarov RK, Solovyev VV.
King Abdullah University of Science and Technology, Thuwal, Saudi Arabia; Softberry Inc., Mount Kisco, United States of America
... genomes. The CNNProm program is available to run at web server http://www.softberry.
com. ... The software to run are available at: http://www.softberry.com/berry.phtml?topic=
index&group=programs&subgroup=deeplearn. Funding ...
Methods In Molecular Biology™
2008 Volume 426 Structural Proteomics: High-throughput Methods (June 10) pp. 37-47 10.1007/978-1-60327-058-8
Target Selection: Triage in the Structural Genomics Battlefield
James Raftery
School of Chemistry, The University of Manchester, Manchester, UK
... events. A mouse-human comparison can be seen at http://www.softberry.
com/berry.phtml?topic=human- mouse&prg=none 1.3. Filters ...
Gene
Volume 316, 16 October 2003, Pages 47-56
The human SUMF1 gene, required for posttranslational sulfatase modification, defines a new gene family which is conserved from pro- to eukaryotes
Jobst Landgrebe1, Thomas Dierks1, Bernhard Schmidt and Kurt von FiguraCorresponding Author Contact Information
Abt. Biochemie II, Universitat Gottingen, Heinrich-Duker-Weg 12, 37073, Gottingen, Germany
... resources (http://www.ncbi.nlm.nih.gov/genome/guide/), the Human-Mouse Homology
Map (http://www.ncbi.nlm.nih.gov/Homology/) and Softberry's Human–Mouse–Rat Synteny (http://www.softberry.
com/). ...
Mammalian Genome
Volume 18, Number 5 / May, 2007 pp. 300-309
Mammary tumor modifiers in BALB/cJ mice heterozygous for p53
Koch et al.,
(1) The University of Texas Graduate School of Biomedical Sciences and the Department of Cancer Genetics, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA
(2) Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA
... SoftBerry’s (http:// www.softberry.com/berry.phtml) Rat-Mouse Synteny for chromosome
1 of rat was used to determine regions of syntenic conservation between ...
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 ...
Acta Physiologiae Plantarum
2017 Jan 1;39(1):40. doi:10.1007/s11738-016-2332-2
Expression pattern and function of wheat mitogen-activated protein kinase (MPK) cascade genes under micronutrient-deprived conditions
Yao S. et al.,
1.College of AgronomyAgricultural University of HebeiBaodingPeople’s Republic of China
2.College of Life SciencesAgricultural University of HebeiBaodingPeople’s Republic of China
... BLASTp provided in NCBI; the protein subcellular localizations after endoplasmic reticulum (ER)
sorted were predicted based on online servers referred to as TargetP 1.1 (http://www.cbs.dtu.
dk/services/TargetP/) and MolQuest-Bioinformatics Toolbox (http://linux1.softberry.com ...
BMC Genomics
2016,17:657 DOI: 10.1186/s12864-016-3017-3
Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity
Bedre, R., Mangu, V. R., Srivastava, S., Sanchez, L. E., & Baisakh, N.
School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center; Department of Genetics and Biochemistry, Clemson University
... The positions
of the SSRs on open reading frames of the genes were determined by using gene finding
software MolQuest (FGENESH+; http://linux1.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. ...
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 ...
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 ...
American Journal of Molecular Biology
2013, 3, 115-130 DOI:10.4236/ajmb.2013.32016
Genome sequencing and next-generation sequence data analysis: A comprehensive compilation of bioinformatics tools and databases
Jose C. Jimenez-Lopez 1, Emma W. Gachomo 2,3, Sweta Sharma 2,3, Simeon O. Kotchoni 2,3
1Department of Biochemistry, Cell and Molecular Biology of Plants, Estacion Experimental del Zaidin, High Council for Scientific Research (CSIC), Granada, Spain
2Department of Biology, Rutgers University, Camden, USA
3Center for Computational and Integrative Biology (CCIB), Rutgers University, Camden, USA
Example of tools used for gene prediction are: 1) Glimmer, a system for finding genes in microbial DNA, especially the genomes of bacteria,
archaea, and viruses (http://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi),
2) FgenesB, a package developed by Soft- berry Inc. for automatic annotation of bacterial genomes
(http://www.molquest.com/help/2.3/programs/FgenesB/about.html),
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). ...
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 Oral Microbiol.
2013; 5: 10.3402/jom.v5i0.19729. DOI:10.3402/jom.v5i0.19729
Cryptic Streptococcus mutans 5.6-kb plasmids encode a toxin–antitoxin system for plasmid stabilization
Anke Rheinberg, 1 Izabela Jadwiga Swierzy, 1 Tuan Dung Nguyen, 1 Hans-Peter Horz, 1,2 and Georg Conrads 1
1Division of Oral Microbiology and Immunology, Department of Operative and Preventive Dentistry & Periodontology, RWTH Aachen University Hospital, Aachen, Germany
2Department of Medical Microbiology, RWTH Aachen University Hospital, Aachen, Germany
... DNA and protein sequences were analyzed with the software programs GeneDoc
(www.psc.edu/biomed/genedoc), Pfam (Sanger Institute, Cambridge, England), MOTIFsearch
(GenomeNet, Kyoto, Japan), Softberry (MolQuest, Mount Kisco, USA), EMBOSS (European ...
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). ...
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...
Australasian Plant Disease Notes
April 2012 DOI
10.1007/s13314-012-0048-8
Clitoria yellow mottle virus: a tobamovirus from Northern Australia
Kejun Wei (1)
Adrian Gibbs (2)
Anne Mackenzie (3)
1. Faculty of Applied Science, University of Canberra, Canberra, ACT, 2617, Australia
2. Australian National University Emeritus Faculty, Canberra, ACT, 0200, Australia
3. CSIRO Division of Plant Industry, Canberra, ACT, 2601, Australia
... The genome of CYMV has the same structure as most other tobamoviruses (Stobbe
et al. 2011). The MolQuest- Softberry viral gene detector (http://www.softberry.com)
found four open reading frames (ORFs) in the CYMV sequence. ...
International Journal of Evolutionary Biology
Volume 2012 (2012), Article ID 970920, 8 pages
doi:10.1155/2012/970920
Purifying Selection Bias against Microsatellites in Gene Rich Segmental Duplications in the Rice Genome
P. C. Sharma, 1 Manish Roorkiwa l,1,2 and Atul Grover 1,3
1University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
2Centre of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad 502324, India
.. [7]. A simple sequence with repeat motif length of 1–6 bp spanning a minimal length
of 20 bp was considered as a microsatellite. Genes were predicted using MolQuest
ver. 1.6.2 (Softberry; http://www.molquest.com/). Following ...
J Gen Virol
November 2011 vol. 92 no. 11 2679-2690 DOI: 10.1099/vir.0.033852-0
The enigmatic genome of Chara australis virus
Gibbs et al.,
Research School of Biological Science, Australian National University, Canberra, ACT 0200, Australia
...ORFs were predicted by using the MolQuest-Softberry viral gene detector, ...
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 ...
Carbohydrate Research
Volume 345, Issue 10, 2 July 2010, Pages 1422-1431 doi:10.1016/j.carres.2010.04.010
Cell surface display of chimeric glycoproteins via the S-layer of Paenibacillus alvei
Zarschler et al.,
Department fur NanoBiotechnologie, Vienna Institute of BioTechnology, Universitat fur Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria
... 50 Bacterial promoters, transcriptional terminators, operons and genes were 1
predicted by the BProm and FindTerm modules of the FGenesB gene prediction
program in 2 Molquest software (SoftBerry, Mount Kisco, NY, USA). ...
Glycobiology
20 (6): 787-798. doi: 10.1093/glycob/cwq035
Protein tyrosine O-glycosylation—A rather unexplored prokaryotic glycosylation system
Zarschler et al.,
Department fur NanoBiotechnologie, Vienna Institute of BioTechnology, Universitat fur Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria
... 2000). Bacterial promoters, transcriptional terminators, operons and ORFs were
predicted by the BProm and FindTerm modules of the FGenesB gene prediction
program in Molquest software (SoftBerry Inc., Mount Kisco, NY). ...
J Bacteriol.
2008 May;190(9):3362-73. Epub 2008 Feb 29.
The sim operon facilitates the transport and metabolism of sucrose isomers in Lactobacillus casei ATCC 334
Thompson J, Jakubovics N, Abraham B, Hess S, Pikis A.
Microbial Biochemistry and Genetics Unit, NIDCR, National Institutes of Health, Bldg. 30, Rm. 325, Convent Dr. MSC-4350, Bethesda, MD 20892, USA
... The structure of operons was predicted by automated genome annotation using
the fgenesB module of the MolQuest software (Softberry Inc.). ...
Journal of Bacteriology
May 2008, p. 3646-3657, Vol. 190, No. 10
Regulation of Gene Expression in a Mixed-Genus Community: Stabilized Arginine Biosynthesis in Streptococcus gordonii by Coaggregation with Actinomyces naeslundii
Nicholas S. Jakubovics,1 Steven R. Gill,2,4 Stacey E. Iobst,4 M. M. Vickerman,2,3 and Paul E. Kolenbrander
National Institute of Dental and Craniofacial Research, National Institutes of Health, Building 30, Room 310, Bethesda, Maryland 20892,1 Department of Oral Biology,2 Department of Periodontics and Endodontics, University at Buffalo School of Dentistry, Buffalo, New York,3 Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 208504
... gordonii genome sequence were detected using the BProm and FindTerm modules of the
fgenesB gene prediction program in Molquest software (Softberry Inc., Mount ...
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. ...
Applied and Environmental Microbiology,
April 2007, p. 2290-2296, Vol. 73, No. 7
The SAR92 Clade: an Abundant Coastal Clade of Culturable Marine Bacteria Possessing Proteorhodopsin
Ulrich Stingl, Russell A. Desiderio, Jang-Cheon Cho, Kevin L. Vergin, and Stephen J. Giovannoni
Oregon State University, Department of Microbiology, Nash Hall 220, Corvallis, Oregon 97331, Division of Life and Marine Sciences, Inha University, Incheon 402-751, Republic of Korea
... of retinal, the chromophore of PR. Operon prediction using MolQuest (SoftBerry,
Inc., Mt. Kisco, NY) software indicated that the ...
Genome Res.
2011. 21: 2224-2241 DOI: 10.1101/gr.126599.111
Assemblathon 1: A competitive assessment of de novo short read assembly methods
Earl et al.,
1Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA;
2Biomolecular Engineering Department, University of California, Santa Cruz, California 95064, USA;
25Softberry Inc., Mount Kisco, New York 10549, USA;
...and OligoZip (http://linux1.softberry.com/berry.phtml?topic=OligoZip). ...
Process Biochemistry
2017 Feb 22 http://dx.doi.org/10.1016/j.procbio.2017.02.018
Chaperone-assisted maturation of the recombinant Fe-type nitrile hydratase is insufficient for fully active expression in Escherichia coli
Zhang H, Li M, Li J, Wang G, Li F, Xiong M.
College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
... Comparisons of the deduced amino acid sequences were performed using the
BLASTP program on the NCBI website. Promoter prediction was carried out using
the Softberry program (http://linux1.softberry.com/all.htm) [21]. ...
Theoretical and Applied Genetics
2017 Jan 1;130(1):71-9. doi:10.1007/s00122-016-2792-1
Map-based cloning of the dominant genic male sterile Ms-cd1 gene in cabbage (Brassica oleracea)
Liang J, Ma Y, Wu J, Cheng F, Liu B, Wang X
Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingPeople’s Republic of China
... 2011, 2015). The new ORF in the region was predicted using the online system Softberry
(http://linux1.softberry.com/berry.phtml). ... S2 Five putative ORFs of the 39.4 kb (B. oleracea) region
identified by Softberry website (PDF 76 kb). 122_2016_2792_MOESM3_ESM.pdf (193 kb) ...
Acta Physiologiae Plantarum
2017 Mar 1;39(3):84. doi:10.1007/s11738-017-2377-x
Cloning and expression of Perilla frutescens FAD2 gene and polymorphism analysis among cultivars
Xue Y. et al.,
Chongqing Key Laboratory of Crop Quality Improvement, Chongqing Engineering Research Center for Rapeseed, College of Agronomy and BiotechnologySouthwest UniversityBeibeiPeople’s Republic of China
... nih.gov/BLAST/). Structure predictions of gene and protein were mainly performed
through links provided by Softberry website (http://linux1.softberry.com/berry.phtml)
and Expasy website (http://cn.expasy.org/tools/). The multi ...
Biotechnology & Biotechnological Equipment
2017 Jan 2;31(1):16-22. http://dx.doi.org/10.1080/13102818.2016.1251828
Efficient gene replacements in ku70 disruption strain of Aspergillus chevalieri var. intermedius
Huang Q, Cao Y, Liu Z, Tan Y, Liu Y.
... The software used for primer design was CODEHOP and Primer premier 5.0. Gene
sequences were analysed using online databases, such as that of the National Cen- ter
for Biotechnology Information (NCBI), ORFfinder, soft- berry and so on. ...
Journal of Biotechnology
2017 Jan 20;242:64-72. http://dx.doi.org/10.1016/j.jbiotec.2016.11.031
Methylotrophic yeast Pichia pastoris as a chassis organism for polyketide synthesis via the full citrinin biosynthetic pathway
Xue Y et al.,
a State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
b Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai 200237, China
... containing complete mpl6 and mpl7 was obtained and sequenced. The coding region
was predicted by Softberry and then confirmed by reverse transcription to harvest
cDNA. The tailoring genes mpl6 and mpl7 were cloned ...
Phytopathology
2017, 107(1), pp.84-91. http://dx.doi.org/10.1094/PHYTO-03-16-0151-R
Fine Mapping of a New Race-Specific Blast Resistance Gene, Pi-hk2, in Japonica Heikezijing from Taihu Region of China
He, W. et al.,
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
... ILP markers were designed around intronic regions which showed higher polymorphism than
exonic regions and were developed according to predicted exons by software tools GENSCAN
(http://genes.mit.edu/?GENSCAN.html) and softberry (http://linux1.softberry.com?/berry ...
Virus Genes
February 2017, Volume 53, Issue 1, pp 146–150. doi:10.1007/s11262-016-1403-1
Complete genome sequence of the lytic cold-active Pseudomonas fluorescens bacteriophage VSW-3 from Napahai plateau wetland
Zhang, C. et al.,
1.Faculty of Life Science and TechnologyKunming University of Science and TechnologyKunmingChina
... program. The Softberry program was used to predict promoter and transcription
termination sites. Open reading frames (ORFs) were predicted using Softberry, Glimmer,
and RAST, and ORFs were confirmed by ORF finder. Functional ...
Trees
2016, 30(4), pp.1033-1043. doi:10.1007/s00468-015-1339-4
Molecular cloning, characterization, and functional analysis of CcBBM gene from camphor tree (Cinnamomum camphora L.)
Liu, Q. et al.,
Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanPeople’s Republic of China
... Sequence analysis and phylogenetic analysis. The full-length CcBBM sequence was analyzed
by DNAMAN v5.0 and ORF finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html). The amino acid
sequence was predicted via Softberry (http://www.softberry.com/). ...
Turkish Journal of Biology
2016, 40(4), pp.889-898.
Identification, characterization, and expression profiling of salt-stress tolerant proton gradient regulator 5 (PGR5) in Gossypium arboreum
SHAHID, M. et al.,
... algorithm (www.ebi.ac.uk/emboss/align). To identify introns, exons, untranslated
regions, and poly-A tails the Softberry server was used (http://www. softberry.com/
berry.phtml). Nucleotide sequences were translated with the ...
Frontiers in Physiology
2016, 7: 413. doi: 10.3389/fphys.2016.00413
Application of Glycerol for Induced Powdery Mildew Resistance in Triticum aestivum L
Li, Y. et al.,
Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
... The primers were designed using DNAMAN software. Putative stress and hormone
responsive cis-regulatory elements were predicted and analyzed using Softberry
(http://linux1.softberry.com/berry.phtml) and SOGO (https://sogo.dna.affrc.go.jp). ...
Journal of Molecular Catalysis B: Enzymatic
2016, 133, pp.167-175. http://dx.doi.org/10.1016/j.molcatb.2016.08.014
Characterization of EstQE, a new member of esterase family VIII from the quizalofop-P-ethyl-degrading bacterium Ochrobactrum sp. QE-9
Zhang, H. et al.,
College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
... SignalP version 4.0 software was used for the identification of potential signal peptides
[19]. Promoter prediction was performed using Softberry (http://linux1.softberry.com/
all.htm) [20]. 2.4. Expression and purification of EstQE. ...
Indonesian Journal of Biotechnology
2016, 20(1), pp.88-97.
Sequences Analysis of a Gene Encoding Extracellular Xylanase in Streptomyces costaricanus 45I-3
Sipriyadi, S., Wahyudi, A.T., Suhartono, M.T. and Meryandini, A.
... was analyzed using BlastX program, Open Reading Frame (ORF) was analyzed using ORF Finder
program on the website of National Center for Biotechnology Information (NCBI), promoter and
Ribosome Binding Site (RBS) were analyzed using program from softberry (www. ...
Plant Cell, Tissue and Organ Culture (PCTOC)
February 2017, Volume 128, Issue 2, pp 457–468 DOI: 10.1007/s11240-016-1123-1
Isolation and functional characterization of a novel stress inducible promoter from pigeonpea (Cajanus cajan L)
Srinath, T., Reddy, V.D. and Rao, K.V.
Centre for Plant Molecular Biology Osmania University Hyderabad India
... http://bioinformatics.psb.ugent.be/webtools/ plantcare/html/) and Softberry
(http://www.softberry.com/) databases. Generation of PCR based CcHyPRP promoter
deletion (834, 477 and 300 bp) fragments A series of 5? deletions ...
Protoplasma
2016 Dec 2:1-15. doi:10.1007/s00709-016-1055-y
Proteins immunologically related to MAP65-1 accumulate and localize differentially during bud development in Vitis vinifera L
Parrotta, L., Faleri, C., Cresti, M. and Cai, G.
Dipartimento Scienze Biologiche, Geologiche e AmbientaliUniversita di BolognaBolognaItaly
Dipartimento Scienze della VitaUniversita di SienaSienaItaly
... The last step was performed to analyze ex-novo prediction of genes (and to confirm the correct
gene prediction by GAZE) using two different online software: Genescan (http://genes.mit.edu/
GENSCAN.html) and Softberry (http://linux1.softberry.com/berry.phtml). ...
Biochemical and Biophysical Research Communications
479, no. 3 (2016): 523-529 http://dx.doi.org/10.1016/j.bbrc.2016.09.103
Identification and analysis of the metacaspase gene family in tomato
Liu, H., Liu, J. and Wei, Y.
a Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
b College of Foreign Languages, Hainan University, Haikou 570228, China
... keyword. Redundant sequences were removed after similarity comparison. The open
reading frames (ORFs) of candidate mRNA or genome DNA sequences were
determined by Softberry (http://linux1.softberry.com/). All identified ...
PloS one
2016, 11(4), e0153962. http://dx.doi.org/10.1371/journal.pone.0153962
Fine Mapping and Candidate Gene Analysis of the Leaf-Color Gene ygl-1 in Maize
Guan, H. et al.,
Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China, Key Laboratory of Biology and Genetic Improvement of North Summer Maize, Ministry of Agriculture, Jinan, China, National Maize Improvement Sub-Center, Jinan, China
.. Gene prediction and annotation within the located region was conducted by
Softberry and according to the Maize Genetics and Genomics Database. ...
Nucleic acids research
2016, 44(6), 2646-2660. doi: 10.1093/nar/gkv1331
Natural C-independent expression of restriction endonuclease in a C protein-associated restriction-modification system
Rezulak, M., Borsuk, I., & Mruk, I.
Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
... possibility of translational coupling. Moreover, the sequence analysis indicated a
potential Rho-independent transcription terminator in the 152-nt intergenic region
separating csp231IR and csp231IM genes (www.softberry.com). ...
Archives of Virology
2016, 1-8. doi:10.1007/s00705-016-3003-8
Molecular epidemiology of J-subgroup avian leukosis virus isolated from meat-type chickens in southern China between 2013 and 2014
Lin, W. et al.,
Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, College of Animal ScienceSouth China Agricultural University, Ministry of Agriculture
Key Laboratory of Animal Health Aquaculture and Environmental Control
South China Collaborative Innovation Center for Poultry Disease Control and Product Safety
... This deletion was similar to the mutation in the 30 UTRs of Chinese ALV-J isolates SCDY1 (Fig.
3). Transcriptional regulation elements were identified in the U3 region of all ALV-J isolates using
SoftBerry software, including C/EBP, E2BP, NFAP-1, CArG box, Y box and CAAT. ...
PloS one
2016, 11(7), e0158159. doi: 10.1371/journal.pone.0158159
Expression Patterns of Three UGT Genes in Different Chemotype Safflower Lines and under MeJA Stimulus Revealed Their Potential Role in Flavonoid Biosynthesis
Guo, D. D. et al.,
Department of Pharmacognosy, College of Pharmacy, Second Military Medical University, 200433, Shanghai, China
... The 3D structures of three UGT proteins were predicted by SWISS
model (beta.swissmodel.expasy.org) (Fig 5). The nucleotide sequence and the deduced amino
acid sequence of three UGTs were predicted (linux1.softberry.com). ...
Scientific reports
2016, 6: 21047. doi: 10.1038/srep21047
Multiple functions of Na/K-ATPase in dopamine-induced salivation of the Blacklegged tick, Ixodes scapularis
Kim, D., Urban, J., Boyle, D. L., Park, Y.
1Department of Entomology, Kansas State University, 123 Waters Hall, Manhattan, KS 66506, USA
2Division of Biology, Microscopy Facility, Kansas State University, Ackert Hall, Manhattan, Kansas 66506, USA
... its homology with other arthropod Na/K-ATPases and
determining the translation initiation site prediction via GeneFinder (www.softberry.com ...
Developmental & Comparative Immunology
2016, 61, 116-125 doi:10.1016/j.dci.2016.03.011
A genome-wide survey of expansive NLR-C subfamily in miiuy croaker and characterization of the NLR-B30.2 genes
Li, J., Chu, Q., Xu, T.
Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
... Che et al., 2014) and whole genome database (Xu et al., 2016) by local BLASTn and tBLASTn
programs. To further confirm the accuracy of miiuy croaker NLR-B and NLR-C subfamily
sequences, the corresponding identified scaffolds were predicted by softberry software. ...
Gene
2016 doi:10.1016/j.gene.2016.07.018
Isolation and molecular characterization of a stationary phase promoter useful for gene expression in Gordonia
Singh, P., Chachan, S., Singhi, D., Srivastava, P.
Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, India
... The secondary structure was predicted by RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.
cgi) and the promoter prediction software used was http://linux1.softberry.com/berry ...
Sains Malaysiana
2016, 45(5), 717-727.
Isolation and Characterization of Full-Length Cellulose Synthase Gene (HsCesA1) from Roselle (Hibiscus sabdariffa L. var. UMKL).
Seyedi, S. S., Tan, S. G., Namasivayam, P., Yong, C. S. Y.
Institute
.. PROMOTER ANALYSIS The promoter
sequence was analyzed using prediction plant promoter (http://linux1.softberry.com/berry.
phtml), neural network promoter prediction (http://www.fruitfly. ...
Molecular plant pathology
2016 DOI: 10.1111/mpp.12444
Fungal phytopathogens encode functional homologues of plant rapid alkalinisation factor (RALF) peptides
Thynne, E. et al.,
Plant Sciences Division, The Australian National University, Canberra, Australia
Evolution, Ecology and Genetics Division, Research School of Biology, The Australian National University, Canberra, Australia
... Masachis et al. (2016) grew plants for inoculation in vermiculite with no plant nutrients provided
and it is possible ... 2013; Nemri et al. 2014). Where annotations were not present or were different,
the online Softberry server (http://linux1.softberry.com/berry.phtml) ...
Arch Virol
2016 doi:10.1007/s00705-016-2965-x
Isolation, identification and evolution analysis of a novel subgroup of avian leukosis virus isolated from a local Chinese yellow broiler in South China
Li, X. et al.,
College of Animal Science, South China Agricultural University
Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture
.. The transcriptional regulatory elements in the non-coding regions of the genome
were analyzed using Softberry (Softberry, Mount Kisco, NY, USA). ...
Plant Physiology and Biochemistry
2016, 108, 241-250. doi:10.1016/j.plaphy.2016.07.016
Molecular cloning and functional characterization of DkMATE1 involved in proanthocyanidin precursor transport in persimmon (Diospyros kaki Thunb.) fruit
Yang, S. et al.,
a Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
b Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang 438000, Hubei, China
c Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
... Translation
of gene sequences was performed using SoftBerry (http://linux1.softberry.com/). ...
Gene
2016, 316, 47-56 doi:10.1016/S0378-1119(03)00746-7
The human SUMF1 gene, required for posttranslational sulfatase modification, defines a new gene family which is conserved from pro-to eukaryotes
Landgrebe, J., Dierks, T., Schmidt, B., von Figura, K.
Abt. Biochemie II, Universitat Gottingen, Heinrich-Duker-Weg 12, 37073 Gottingen, Germany
.. and
mouse genome resources (http://www.ncbi.nlm.nih.gov/genome/guide/), the Human–Mouse
Homology Map (http://www.ncbi.nlm.nih.gov/Homology/) and Softberry's Human–Mouse ...
BMC genetics
2016, 17(1), 1. DOI: 10.1186/s12863-016-0350-0
DHPLC technology for high-throughput detection of mutations in a durum wheat TILLING population
Colasuonno, P. et al.,
Department of Soil, Plant and Food Sciences, section of Genetic and Plant Breeding, University of Bari "Aldo Moro"
... All these sequences were subjected to bioinformatic analysis via Aegilops tauschii genome
sequence database [42] and CerealsDB site [43] to distinguish the A and B genome
homoeologous copies, and via SoftBerry [44] to predict the gene structures. ..
Research in microbiology
2016, 167(5), 403-412. doi:10.1016/j.resmic.2016.03.005
The arginine deiminase system facilitates environmental adaptability of Streptococcus equi ssp. zooepidemicus through pH adjustment
Xu, B. et al.,
a College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
b Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
... According to the results of in silico analysis (Softberry, www.softberry.com), a promoter and a
terminator were predicted to be located in the intergenic region between arcB and arcD, which
indicated that arcA, orf2 and arcB, or arcD, arcT and arcC might also be transcribed as an ...
Advanced Science Letters
2016, 10(1), 146-152. DOI: http://dx.doi.org/10.1166/asl.2012.3743
Cloning and Bioinformatics Analysis of a Peroxidase Gene from Camellia Oleifera Seed
Chen, H., Tan, X., Shao, G.
Institute
... Second Structure Analysis and 3D Structure Prediction The Softberry Platform figured out that
-helix and -sheet were the main components in the second structure of Co-POD, and there ... IP:
93.91.26.12 On: Sun, 20 Mar 2016 03:18:59 Copyright: American Scientific Publishers ...
Gene
Volume 580, Issue 1, 10 April 2016, Pages 8–16 doi:10.1016/j.gene.2015.12.069
Molecular cloning, expression and characterization of acylpeptide hydrolase in the silkworm, Bombyx mori
Fu, P., Sun, W., Zhang, Z.
School of Life Sciences, Chongqing University, Chongqing 400044, China
... Therefore, we re-predicted the APH gene in the scaffold 2829 on the 17th chromosome of silkworm
using softberry (www.softberry.com). Based on the nucleotide sequence of the putative APH gene,
the specific primers were designed to clone the gene (Table S1). ...
Tree Genetics & Genomes
2016, 12(2), 1-11. DOI: 10.1007/s11295-016-0976-0
ADH and PDC genes involved in tannins coagulation leading to natural de-astringency in Chinese pollination constant and non-astringency persimmon (Diospyros kaki Thunb.)
Mo, R. et al.,
1. Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China
2. Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang, 438000, China
... The gene sequences were confirmed with BLAST in GenBank. The ORFs of genes were predicted
using online software (http://?linux1.?softberry.?com/?). Sequence identity analysis was
performed with ClustalW2 (Khater et al. 2012). RNA extraction and qRT-PCR analysis. ...
Scientific reports
2016, 6: 19104. doi: 10.1038/srep19104
A Novel Naturally Occurring Class I 5-Enolpyruvylshikimate-3-Phosphate Synthase from Janibacter sp. Confers High Glyphosate Tolerance to Rice
Yi, S. Y. et al.,
1State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
2National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
... Sequence analysis. The inserted fragment from the plasmid pZY3 was sequenced by the
Genescript Company (Nanjing, China), and the nucleotide sequences were analyzed using
the Softberry Gene Finding Tool (http://linux1.softberry.com/berry). ...
Developmental & Comparative Immunology
2016, 61, 116-125. doi:10.1016/j.dci.2016.03.011
A genome-wide survey of expansive NLR-C subfamily in miiuy croaker and characterization of the NLR-B30. 2 genes
Li, J., Chu, Q., Xu, T.
Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
... To further confirm the accuracy of miiuy croaker NLR-B and NLR-C subfamily sequences, the
corresponding identified scaffolds were predicted by softberry software. The cDNA sequences
were aligned with the obtained scaffold using MAFFT (Katoh and Standley, 2013). 2.5. ...
FEMS microbiology letters
2016, 363(8), fnw063. DOI: http://dx.doi.org/10.1093/femsle/fnw063
Overexpression of two stress-responsive, small, non-coding RNAs, 6S and tmRNA, imparts butanol tolerance in Clostridium acetobutylicum
Jones, A. J., Venkataramanan, K. P., Papoutsakis, T.
1Department of Biological Sciences, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
2Molecular Biotechnology Laboratory, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
... The larger bands present in both tmRNA and 6S RNA northern blots are believed to be
transcriptional products from additional promoters on the p94MCS vector backbone located
upstream of its cloning site; using the Softberry promoter prediction tool (Solovyev and Salamov ...
Frontiers in plant science
2016, 7: 156. doi: 10.3389/fpls.2016.00156
Isolation and Characterization of DkPK Genes Associated with Natural Deastringency in C-PCNA Persimmon
Guan, C. et al.,
1Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China
2Institute of Horticultural Sciences, Jiangxi Academy of Agricultural Sciences, Nanchang, China
... The sequences of the primers used for RACE, genome walking and cloning are described in
Supplementary Table S1. The gene sequences were translated with online software
(http://linux1.softberry.com/) and confirmed with BLAST methods in GenBank (Benson et al., 2000). ...
Journal of Integrative Agriculture
2016 Doi: 10.1016/S2095-3119(15)61295-3
Isolation and molecular characterization of the FLOWERING LOCUS C gene 2 promoter sequence in radish (Raphanus sativus L.).
Rong-hua, L. U. O., Li-wang, L. I. U.
1National Key Laboratory of Crop Genetics and Germplasm Enhancement; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), M
inistry of Agriculture of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China.
2 Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA.
... The promoter's' transcription start sites (TSS) were predicted by the Softberry databases ...
Research in microbiology
2016, Volume 167, Issue 5, June 2016, Pages 403–412 doi:10.1016/j.resmic.2016.03.005
The arginine deiminase system facilitates environmental adaptability of Streptococcus equi ssp. zooepidemicus through pH adjustment
Xu, B. et al.,
a College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
b Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
... According to the results of in silico analysis (Softberry, www.softberry.com), a promoter and a
terminator were predicted to be located in the intergenic region between arcB and arcD, which
indicated that arcA, orf2 and arcB, or arcD, arcT and arcC might also be transcribed as an ...
PloS one, 11(3), e0151657. http://dx.doi.org/10.1371/journal.pone.0151657
2016
KatG, the Bifunctional Catalase of Xanthomonas citri subsp. citri, Responds to Hydrogen Peroxide and Contributes to Epiphytic Survival on Citrus Leaves
Tondo, M. L. et al.,
Molecular Biology Division, Instituto de Biologia Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Cientificas y Tecnicas, Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
Planta Piloto de Procesos Industriales Microbiologicos, Consejo Nacional de Investigaciones Cientificas y Tecnicas, San Miguel de Tucuman, Tucuman, Argentina
... bp upstream of the 5' end to 22 bp downstream of the 3' end of the ORF was amplified using the
primer pair ckatG-F and ckatG-R (Table 1). The amplified sequence included the putative promoter
sequence of the katG gene, previously predicted with SoftBerry (www.softberry ...
Horticultural Plant Journal
2016, Volume 2, Issue 1, Pages 16–25 doi:10.1016/j.hpj.2016.02.001
Evolution of TWIN SISTER of FT (TSF) Genes in Brassicaceae
Hu, Y. et al.,
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
... syntenic intergenic regions). Residues present in intergenic regions were
re-annotated using SoftBerry (http://linux1.softberry.com/). 3. Results. 3.1. Identification
of FT and TSF genes in Brassicaceae genomes. FT orthologs in ...
Scientific reports
2016, 6: 20532. doi: 10.1038/srep20532
Transcriptional Regulation of Atp-Dependent Chromatin Remodeling Factors: Smarcal1 and Brg1 Mutually Co-Regulate Each Other
Haokip, D. T. et al.,
1Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067.
... gene was analyzed for its regulatory sequences. Bioinformatic analysis using
Softberry promoter prediction software (www.softberry.com) as well as information
from Huang et al. 23 showed that a putative promoter sequence was present upstream of the translation start
sequence and the promoter region was enriched in CpG islands....
Planta
2016, 1-11. DOI 10.1007/s00425-016-2511-9
Identification and functional characterization of the NAC gene promoter from Populus euphratica
Wang, J. Y., Wang, J. P., Yang, H. F.
1. Biotechnology Research Institute of the Chinese Academy of Agricultural Sciences, No. 12 Zhong Guan Cun South Street, 100081, Beijing, China
2. Tianjin University of Science and Technology, No. 29 13th Avenue, Tianjin Economic and Technological Development Area, 300457, Tianjin, China
... The transcription start site was analyzed using available online tools (http://?www.?Softberry.?
com). ... The elements were identified using PLACE. The transcription start site analysis was
completed using online tools (http://?www.?Softberry.?com). ...
Plant Physiology and Biochemistry
2016, 105, 90-101. doi:10.1016/j.plaphy.2016.04.011
Genome-wide identification and expression analysis of the metacaspase gene family in Hevea brasiliensis
Liu, H. et al.,
a Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
b College of Agriculture, Hainan University, Haikou 570228, China
... Redundant sequences were removed after similarity comparison. The open reading frames
(ORFs) of candidate mRNA or genome DNA sequences were determined by NCBI ORF Finder
(http://www.ncbi.nlm.nih.gov/gorf/gorf.html) and Softberry (http://linux1.softberry.com/). ...
Pakistan Journal of Agricultural Sciences
2016, 53(1), 27-33.
Characterization of ERD15 gene from cultivated tomato (Solanum lycopersicum).
Ziaf, K. et al.,
... Bioinformatics analyses: The sequencing results were used to get predicted peptide for SlERD15
using Genescan (MIT, Cambridge, MA) and Softberry. Intron in the genomic DNA was computed
by the Splign tool at NCBI (http://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi). ...
Virus Genes
2016, Volume 52, Issue 3 , pp 432-435 DOI: 10.1007/s11262-016-1300-7
Complete genome sequence of the cold-active bacteriophage VMY22 from Bacillus cereus
Qin K. et al.,
1. Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China
2. Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
... The Tandem Repeats Finder program was used to test for the presence of tandem repeats. Open
reading frames (ORFs) were predicted using program Softberry and RAST. ... The program Softberry
was used to predict promoter and transcription termination sites. ...
FEMS microbiology letters
2015, 362(16), fnv107. DOI: http://dx.doi.org/10.1093/femsle/fnv107
Isolation of strong constitutive promoters from Lactococcus lactis subsp. lactis N8
Zhu, D. et al.,
College of Life Sciences, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
Department of Food and Environmental Sciences, University of Helsinki, Finland
... Then the promoters of corresponding genes were analysed by SoftBerry software
(http://www.softberry.com) and amplified by PCR with the L. lactis N8 chromosomal DNA as the
template using the primer pairs P1-F/P1-R, P2-F/P2-R, P3-F/P3-R, P4-F/P4-R, P5-F/P5-R, P6- ...
FEMS microbiology ecology
2015, 91(7), fiv071. DOI: http://dx.doi.org/10.1093/femsec/fiv071
Cellulose production in Pseudomonas syringae pv. syringae: a compromise between epiphytic and pathogenic lifestyles
Arrebola, E. et al.,
Instituto de Hortofruticultura Subtropical y Mediterranea ‘La Mayora’, Universidad de Malaga, Consejo Superior de Investigaciones Cientificas, Estacion Experimental La Mayora, Algarrobo-Costa, 29750 Malaga, Spain
Centro de Biotecnologia y Genomica de Plantas UPM-INIA, Parque Cientifico y Tecnologico de la Universidad Politecnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcon, Madrid, Spain
... GC analyses, promoter, terminator and IS (insertion sequence) analyses, and primer design were
performed using a GC calculator (http://www.genomicsplace.com/gc_calc.html), SoftBerry
(http://linux1.softberry.com/berry.phtml), IS Finder (http://www-is.biotoul.fr) and Primer3 ...
Plant Systematics and Evolution
2015, 301:211-216 doi:10.1007/s00606-014-1066-0
Classification of cytochrome P450s in common bean (Phaseolus vulgaris L.)
M. Shailendar Kumar et al.,
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. ...
International journal of biological macromolecules
2015, 79, 952-964. http://dx.doi.org/10.1016/j.ijbiomac.2015.05.038
A novel keratinase from Bacillus tequilensis strain Q7 with promising potential for the leather bating process
Jaouadi, N. Z. et al.,
a Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia
b Laboratory of Natural Products Chemistry and Biomolecules (LNPCB), University of Blida, 1, Road of Soumaa, P.O. Box 270, 09000 Blida, Algeria
... DNASTAR Inc., Madison, WI, USA) software packages. The nucleotide sequences
data were analyzed using the Softberry Gene Finding tool (http://linux1.softberry.com/
berry.phtml). The 16S rRNA sequence analysis was performed ...
Applied biochemistry and biotechnology
2015, 175(3), 1344-1357. doi:10.1007/s12010-014-1277-4
Cloning and characterization of a multifunctional promoter from Maize (Zea mays L.)
Dong, Q. et al.,
Key Lab of Biomass Improvement and ConversionAnhui Agricultural University
... Acting Regulatory Elements (PlantCARE) (http://?bioinformatics.?psb.?ugent.?be/?webtools/?
plantcare/?html/?) [33] and PLACE (http://?www.?dna.?affrc.?go.?jp/?PLACE/?) [20], and
the transcription star site (TSS) was predicted at the website (http:// linux1.softberry.com ...
Proceedings of the National Academy of Sciences, India Section B: Biological Sciences
June 2013 DOI:10.1007/s40011-013-0192-8
Organization and Classification of Cytochrome P450 Genes in Castor (Ricinus communis L.)
Maryada Shailendar Kumar, Peram Ravindra Babu, Khareedu Venkateswara Rao, Vudem Dashavantha Reddy
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. ...
Gene
Volume 528, Issue 2, 10 October 2013, Pages 170–177 DOI: 10.1016/j.gene.2013.07.022
PLC-?1-Lf, a novel N-terminal extended phospholipase C-?1
Kim et al.,
a Department of Aquatic Life Medicine, Pukyong National University, Busan 608-737, South Korea
b Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
... The promoter region was predicted from the genomic DNA sequence using BIMAS Promoter
Scan Version 1.7 (http://bimas.dcrt.nih.gov/molbio/proscan/), Softberry (http://www.softberry.com/),
Promoter 2.0 Prediction (http://www.cbs.dtu.dk/services/Promoter/), and MOTIF Search ...
Molecular Biology Reports
April 2013, Volume 40, Issue 4, pp 2887-2896 DOI:10.1007/s11033-012-2304-6
Comparative characterization of sweetpotato antioxidant genes from expressed sequence tags of dehydration-treated fibrous roots under different abiotic stress conditions
Yun-Hee Kim, Jae Cheol Jeong, Haeng-Soon Lee, Sang-Soo Kwak
1. Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon, 305-806, Republic of Korea
... The isoelectric point (pI), molecular weight, and signal sequences of deduced proteins were
predicted using the ExPasy (http://www.expasy.org/tools), PSORT (http://psort.ims.u-tokyo.ac.
jp), and SoftBerry (http://www.softberry.com) programs. Stress treatment. ...
Current Microbiology
Volume 66, Issue 3 , pp 259-265 DOI: 10.1007/s00284-012-0266-5
Identification of Regulatory Sequences and Expression Analysis of OmpR Gene Under Different Stress Conditions in the Antarctic Bacterium Psychrobacter sp. G
Weizhi Song, Xuezheng Lin, Shuai Che
1. Key Lab of Marine Bioactive Substances, First Institute of Oceanography, SOA, Xianxialing Road 6, Qingdao, 266061, China
... Bioinformatics Analysis of OmpR503 The regulatory sequences, ie, -10 region, -35
region, ribosomal binding site (RBS), and open reading frame (ORF) were analyzed
using the Softberry (http://linux1. softberry.com/berry.phtml ...
J. Agric. Food Chem.
2013, 61 (26), pp 6423–6429
DOI: 10.1021/jf401537q
A Vigna radiata 8S Globulin ?? Promoter Drives Efficient Expression of GUS in Arabidopsis Cotyledonary Embryos
Chen et al.,
† College of Life Science, Jinan University, Guangzhou 510632, China
‡ School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
... The transcription start site and TATA box were 126 predicted with software Softberry
(http://www.softberry.com). ... 32 Putative 188 cis-elements were identified and analyzed using
several promoter analysis software including 189 plantCARE, PLACE and Softberry. ...
World Journal of Microbiology and Biotechnology
September 2013 DOI:10.1007/s11274-013-1477-z
Cloning and characterization of squalene synthase gene from Poria cocos and its up-regulation by methyl jasmonate
Wang et al.,
1. Department of Bioengineering, College of Food Science, South China Agricultural University, 482 Wu-Shan Road, Tian-He District, Guangzhou, 510642, Guangdong, China
3. Guangdong VTR Bio-Tech Co., Ltd., Zhuhai, China
... Further analyses of the sequences were performed by using Recognition of Regulatory Motifs
with statistics in the softberry software (http://www.softberry.rn/berry.html) and PLACE Web
Signal Scan (http://www.dna.affrc.go.jp/PLACE/signalscan.html). ...
Appl. Environ. Microbiol.
October 2013 vol. 79 no. 19 6176-6179 DOI:10.1128/AEM.02015-13
Clostridium acidurici Electron-Bifurcating Formate Dehydrogenase
Shuning Wang a,b, Haiyan Huang a, Jorg Kahnt a and Rudolf K. Thauer a
Max Planck Institute for Terrestrial Microbiology, Marburg, Germanya
State Key Laboratory of Microbial Technology, Shangdong University, Jinan, People's Republic of Chinab
... terminator. Bioinformatics analysis was performed with Softberry software (Softberry,
Inc., NY) and the software provided by the ARNold finding terminators at IGM-Web
Server (http://rna.igmors.u-psud.fr/toolbox/arnold/index.php). ...
AAC
00423-13 May 2013, doi: 10.1128/AAC.00423-13
Complete Sequence of pOZ176, a 500-kb IncP-2 Plasmid Encoding IMP-9-mediated Carbapenem Resistance, from Outbreak Isolate Pseudomonas aeruginosa 96
Xiong et al.,
aDept. of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
bPublic Health Ontario Laboratories, Toronto, ON, Canada
cCentre de Recherche en Infectiologie, CHU de Quebec, Quebec, QC, Canada
... Additional software, including IS finder 119 (http://www-is.biotoul.fr/is.html) and various Softberry
programs 120 (http://linux1.softberry.com/berry.phtml), were used for analysis of specific plasmid
genetic 121 features, such as IS elements and pathogenicity islands. ...
Functional & Integrative Genomics
Volume 13, Issue 4 , pp 425-434 DOI:10.1007/s10142-013-0333-4
Genes encoding the production of extracellular polysaccharide bioflocculant are clustered on a 30-kb DNA segment in Bacillus licheniformis
Yan et al.,
1. Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People’s Republic of China
2. Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, 361005, People’s Republic of China
... DNA sequencing was performed by Majorbio BioTechnologies Co., Ltd. (Shanghai, China).
The open reading frames (ORFs) and predicted genes in the DNA sequences were identified
using the SoftBerry program (http:// linux1.softberry.com/berry.phtml). ...
PloS one
April 09, 2013DOI: 10.1371/journal.pone.0060717
Klebsiella Phage vB_KleM-RaK2 — A Giant Singleton Virus of the Family Myoviridae
Simoliunas et al.,
Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
... sequences was performed using extractUpStreamDNA (http://lfz.corefacility.ca/extractUpStre?
amDNA/), MEME analysis [36] at http://meme.sdsc.edu/meme/cgibin/meme.cg?i as well as
PePPER (http://pepper.molgenrug.nl/index.php/pep?per-tools) and SoftBerry (http://linux1 ...
Neurosignals
2013;21:129-149 (DOI:10.1159/000343672)
Brain-Site-Specific Proteome Changes Induced by Neuronal P60TRP Expression
Manavalan A. a, b · Mishra M. a, b · Sze S.K. a · Heese K. c
aSchool of Biological Sciences and bInstitute of Advanced Studies, Nanyang Technological University, Singapore, Singapore; cDepartment of Biomedical Engineering, Hanyang University, Seoul, Korea
... picture [10]. We used online databases, eg Panther (www.pantherdb.org), UniProt,
NCBI, and 'softberry' (http://linux1.softberry.com/ berry.phtml), to classify the functions
of the iTRAQ-identified p60TRP-regulated proteins. STRING ...
Genes & Genomics
Volume 35, Issue 1 , pp 47-58 DOI:10.1007/s13258-013-0068-6
Cloning and characterization of Tc1 family-derived PPTN related transposons from ridged-eye flounder (Pleuronichthys cornutus) and inshore hagfish (Eptatretus burgeri)
Sang Jung Ahn et al.,
1. Department of Biotechnology, Pukyong National University, Busan, 608-737, South Korea
2. Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
... and Ensembl Multi blastview. Promoter regions in transposons were identified using
BIMAS Promoter Scan Version 1.7 (http://bimas.dcrt. nih.gov/molbio/proscan/),
Softberry (http://www.softberry. com/),Promoter 2.0 Prediction ...
Journal of Asia-Pacific Entomology
Volume 16, Issue 3, September 2013, Pages 257–261 DOI:10.1016/j.aspen.2013.03.004
Characterization of a novel mosquitocidal strain of Bacillus thuringiensis serovar aizawai which harbors a rolling-circle replication plasmid, pBt1–3
Liu et al.,
a Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-742, Republic of Korea
b Division of Medical Entomology, Korea National Institute of Health, Chungbuk 363-951, Republic of Korea
... nih.gov/gorf/gorf.html) and Softberry (http://linux1.softberry.com/berry.phtml) were utilized to predict
the putative open reading frames (ORFs) of pBt1-3. The plasmid pBt1-3 nucleotide sequence
determined in this paper has been deposited in the GenBank database under the ...
Scientia Horticulturae
Volume 156, 7 June 2013, Pages 29–37 DOI:10.1016/j.scienta.2013.03.003
Functional analysis of female gametophyte specific promoters in Chinese cabbage
Soo-Yun Kim a, Hee-Ju Yu b, Joon Ki Hong c, Jong Gyu Woo a, Yul Kyun Ahn a
a Vegetable Research Division, National Institute of Horticultural and Herbal Science, RDA, Suwon 440-706, Republic of Korea
b Department of Life Sciences, the Catholic University of Korea, Buxheon 420-743, Republic of Korea
... Sequence information of At5g40260 was obtained from the National Center for Biotechnology
Information (NCBI) (http://www.ncbi.nlm.nih.gov/). Hypothetical coding sequences of At5g40260
and BRA0029160 were predicted using Softberry program (www.softberry.com). ...
Journal of Agricultural Science and Technology
Article 16, Volume 16, Issue 1, January 2014, Page 191-202
Isolation and Characterization of DBR2 Gene Promoter from Iranian Artemisia annua
R. Sarvestani; S. A. Peyghambary; A. Abbasi
Department of Agronomy and Plant Breeding, Agricultural College, University of Tehran, Karaj, Islamic Republic of Iran.
... DNA sequencing was performed on an ABI 373A automated sequence. Then, promoter prediction,
characterization, and search for the putative cis-acting elements were carried out using different
databases: Softberry, PlantCARE [23] and PLACE [24]. Page 4. ...
Applied Biochemistry and Biotechnology
Volume 169, Issue 3 , pp 950-959 DOI: 10.1007/s12010-012-0060-7
Selective n-Butanol Production by Clostridium sp. MTButOH1365 During Continuous Synthesis Gas Fermentation Due to Expression of Synthetic Thiolase, 3-Hydroxy Butyryl-CoA Dehydrogenase, Crotonase, Butyryl-CoA Dehydrogenase, Butyraldehyde Dehydrogenase, and NAD-Dependent Butanol Dehydrogenase
Vel Berzin, Michael Tyurin, Michael Kiriukhin
1. Syngas Biofuels Energy, Inc., 2441 Del Monte, Houston, TX, 77019, USA
2. Ajinomoto–Genetika Research Institute, 1st Dorozhny pr. 1-1, 117545, Moscow, Russia
... Promoter and terminator sequences for the components of all vectors were identified using
SoftBerry Bacterial Promoter, Operon and Gene Finding tool (http://linux1.softberry.com/).
Electrotransformation procedure [7] was used in modification. ...
PloS one
March 29, 2013DOI: 10.1371/journal.pone.0059802
Truncated Cotton Subtilase Promoter Directs Guard Cell-Specific Expression of Foreign Genes in Tobacco and Arabidopsis
Lei Han, Ya-Nan Han, Xing-Guo Xiao
State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
... Online analysis using SoftBerry (http://linux1.softberry.com) and PLACE (http://www.dna.affrc.
go.jp/htdocs/PLACE/) [60] of the regulatory fragment revealed the presence of 1 TATA box
(?31) and 10 Dof protein-targeted cis-acting elements “(T/A)AAAG” (Fig. ...
Experimental & Molecular Medicine
2013) 45, e39; doi:10.1038/emm.2013.76 Published online 6 September 2013
Brain site-specific proteome changes in aging-related dementia
Manavalan et al.,
1School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
2Department of Obstetrics and Gynecology, University of California Irvine, Irvine, CA, USA
... In addition, we used online databases (for example, Panther (Protein Analysis Through
Evolutionary Relationship) at www.pantherdb.org, UniProt, NCBI and 'softberry' http://linux1.
softberry.com/berry.phtml) to classify the functions of the iTRAQ-identified proteins modulated ...
J. Exp. Zool. (Mol. Dev. Evol.) .
9999:1–11 DOI: 10.1002/jez.b.22527
Transcriptional activity of transposable elements in coelacanth
Forconi et al.,
1Dipartimento di Scienze della Vita e dell'Ambiente, Universita Politecnica delle Marche, Ancona, Italy
2Institut de Genomique Fonctionnelle de Lyon, ENS Lyon, France
tools, such as Censor (Jurka et al., 1996, 2005), BLAST (Altschul et al., 1990), Softberry
(http://linux1.softberry.com/berry.phtml), RNAfold (http://rna.tbi.univie.ac.at), and MUSCLE ...
Plant Science
Volume 213, December 2013, Pages 106–113 DOI:10.1016/j.plantsci.2013.09.005
The tonoplast intrinsic aquaporin (TIP) subfamily of Eucalyptus grandis: Characterization of EgTIP2, a root-specific and osmotic stress-responsive gene
Marcela I. Rodrigues, Juliana P. Bravo, Flavio T. Sassaki, Fabio E. Severino, Ivan G. Maia
UNESP, Instituto de Biociencias, Departamento de Genetica, Botucatu, SP, Brazil
... and [27]. The transcriptional start site (TSS) prediction program [28] available at Softberry
(www.softberry.com) was used to predict the TSS position of EgTIP2. 2.11. Generation
of transgenic tobacco plants. The resulting pCAMBIAEgTIPpromo ...
The Crop Journal
Volume 1, Issue 1, October 2013, Pages 2–14 DOI:10.1016/j.cj.2013.07.007
Identification and fine mapping of two blast resistance genes in rice cultivar 93-11
Lei et al.,
a Institute of Crop Science, Chinese Academy of Agricultural Sciences, The National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
b Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Provincial Center of Plant Gene Engineering, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
... Ltd., Beijing. DNA and protein sequences were predicted using the softberry program
(http://linux1.softberry.com/), and then aligned with Nipponbare homologues using the
Gramene and EBI needle programs (http://www.ebi.ac.uk/). Table 4. ...
Journal of Integrative Plant Biology
DOI:10.1111/jipb.12144
SbHKT1;4, a member of the high affinity potassium transporter gene family from Sorghum bicolour, functions to maintain optimal Na+/K+ balance under Na+ stress
Wang et al.,
1The Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
2College of Life Sciences, Capital Normal University, Beijing, China
... bright border fluorescence, which was consistent with the cell membrane-localised prediction
by TMHMM server and the softberry online database (www.softberry.com). To determine whether
the expression of the SbHKT1;4 was modulated by the external ...
Plant Molecular Biology Reporter
Volume 31, Issue 5 , pp 1176-1183 DOI:10.1007/s11105-013-0576-1
Structural and Transcriptional Characterization of rbcS Genes of Cotton (Gossypium hirsutum)
Kumar Paritosh, Deepak Pental, Pradeep Kumar Burma
1. Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
2. Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
... Higo et al. 1999), PlantCARE (Lescot et al. 2002), and Softberry (www.softberry.com.)
databases. A number of putative regulatory motifs corresponding to the known
cis-elements of rbcS genes were found. The relative positions ...
Journal of Industrial Microbiology & Biotechnology
Volume 40, Issue 7 , pp 749-758 DOI:10.1007/s10295-013-1279-1
Gene replacement and elimination using ?Red- and FLP-based tool to re-direct carbon flux in acetogen biocatalyst during continuous CO2/H2 blend fermentation
Michael Tyurin
1. Syngas Biofuels Energy, Inc., P.O. Box 300819, Houston, TX, 77230, USA
... Promoter and terminator sequences. Promoter and terminator sequences used in both vectors
were identified using Softberry Bacterial Promoter, Operon and Gene Finding tool
(http://linux1.softberry.com/). Primers for the synthetic genes used in this project are listed in Table ...
World Journal of Microbiology and Biotechnology
Volume 29, Issue 9 , pp 1611-1623 DOI:10.1007/s11274-013-1324-2
Selective methanol or formate production during continuous CO2 fermentation by the acetogen biocatalysts engineered via integration of synthetic pathways using Tn7-tool
Michael Tyurin, Michael Kiriukhin
1. Syngas Biofuels Energy, Inc., P.O. Box 300819, Houston, TX, 77230, USA
2. Ajinomoto-Genetika Research Institute, 1st Dorozhny Pr. 1-1, 117545, Moscow, Russia
... early sporulation gene. Promoter and terminator sequences for the components of
all vectors used were identified using SoftBerry Bacterial Promoter, Operon and Gene
Finding tool (http://linux1.softberry.com/). The confirmation ...
Bioprocess Biosyst Eng.
2013 Jun 18. DOI:
Mevalonate production by engineered acetogen biocatalyst during continuous fermentation of syngas or CO2/H 2 blend.
Kiriukhin M, Tyurin M.
Syngas Biofuels Energy, Inc., P.O. Box 300819, Houston, TX, 77230, USA.
... Promoter and terminator sequences for the components of all vectors. Promoter and terminator
sequences for the components of all vectors were identified using SoftBerry Bacterial Promoter,
Operon and Gene Finding tool (http://linux1.softberry.com/). RT-PCR. ...
Journal of Applied Microbiology
Volume 114, Issue 4, pages 1033–1045, April 2013 DOI:10.1111/jam.12123
Expression of amplified synthetic ethanol pathway integrated using Tn7-tool and powered at the expense of eliminated pta, ack, spo0A and spo0J during continuous syngas or CO2/H2 blend fermentation
M. Kiriukhin 1, M. Tyurin 2,
1Ajinomoto-Genetika Research Institute, Moscow, Russia
2Syngas Biofuels Energy, Inc, Houston, TX, USA
... Promoter and terminator sequences for the components of all vectors. Promoter and terminator
sequences for the components of all vectors were identified using SoftBerry Bacterial Promoter,
Operon and Gene Finding tool (http://linux1.softberry.com/). rtPCR. ...
Applied Biochemistry and Biotechnology
Volume 170, Issue 6 , pp 1503-1524 DOI:10.1007/s12010-013-0285-0
Synthetic 2,3-Butanediol Pathway Integrated Using Tn7-tool and Powered Via Elimination of Sporulation and Acetate Production in Acetogen Biocatalyst
Michael Tyurin, Michael Kiriukhin
State
... Promoter and Terminator Sequences for the Components of All Vectors Promoter and terminator
sequences for the components of all vectors were identified using SoftBerry Bacterial Promoter,
Operon and Gene Finding tool (http://linux1.softberry.com/). RT-PCR ...
Theoretical and Applied Genetics
Volume 126, Issue 5 , pp 1273-1283 DOI:10.1007/s00122-013-2052-6
Structure, transcription and post-transcriptional regulation of the bread wheat orthologs of the barley cleistogamy gene Cly1
Ning et al.,
1. Plant Genome Research Unit, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
2. Graduate school of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
... cgi). Softberry Bacterial Genome Explorer (http://www.linux1.softberry.com/berry.
phtml) software was then used to allow the simultaneous comparison of distinct
annotated genomes. Phylogenetic analysis. Protein sequence ...
Antimicrob. Agents Chemother.
April 2013 vol. 57 no. 4 1603-1609 DOI:10.1128/AAC.01998-12
Elucidating the Regulon of Multidrug Resistance Regulator RarA in Klebsiella pneumoniae
Shyamasree De Majumdar a, Mark Veleba a, Sarah Finn b, Seamus Fanning b and Thamarai Schneiders a
aCentre for Infection and Immunity, Queen's University Belfast, Belfast, United Kingdom
bUCD Centre for Molecular Innovation and Drug Design, School of Public Health, Physiotherapy & Population Science, University College Dublin, Dublin, Ireland
... labeled “TSS” and shaded. The Shine-Dalgarno sequence is shown underlined, and
putative ?10, ?35 promoter regions determined through Softberry software analysis
are shown boxed and labeled accordingly. Our initial work ...
Genetic Testing and Molecular Biomarkers.
July 2013, 17(7): 553-561. doi:10.1089/gtmb.2012.0118.
Results of Genetic Testing in 855 Consecutive Unrelated Patients Referred for Long QT Syndrome in a Clinical Laboratory
Lieve et al.,
1Department of Pediatrics, Columbia University, New York, New York.
2Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
3GeneDx, Gaithersburg, Maryland.
... Browser. Variants were analyzed for predicted functional effect using PolyPhen2,
SIFT, Mutation Taster, Softberry Grantham score, cross species alignment, and location
compared with published functional domains of the protein. ...
Microbial Biotechnology,
6: 551–563. (2013) doi: 10.1111/1751-7915.12040
Tight coupling of polymerization and depolymerization of polyhydroxyalkanoates ensures efficient management of carbon resources in Pseudomonas putida.
Arias, S., Bassas-Galia, M., Molinari, G. and Timmis, K. N.
1Environmental Microbiology Laboratory, Helmholtz Centre for Infection Research, Braunschweig, Germany
2Institute for Microbiology, Technical University Braunschweig, Braunschweig, Germany
... The analysis of possible transcription promoters using Softberry, PromScan and the PDBG online
informatics tools, revealed that all pha genes are preceded by potential promoters and more
specifically, that both ? 70 and ? 54 potential promoters were found upstream of the ...
J. Bacteriol.
December 2013 vol. 195 no. 23 5233-5241 DOI:10.1128/JB.00965-13
Expanding the Cyanuric Acid Hydrolase Protein Family to the Fungal Kingdom
Anthony G. Dodge a, Chelsea S. Preiner a and Lawrence P. Wacket a,b
BioTechnology Institutea
Department of Biochemistry, Molecular Biology, and Biophysics,b University of Minnesota, St. Paul, Minnesota, USA
... directions by DNA sequence walking with a GenomeWalker Universal kit (Clontech, Mountain
View, CA) and primers SaroGSP1-5?, SaroGSP1-3?, SaroGSP2-5?, and SaroGSP2-3? (Table
1). Potential genes were predicted in the resulting sequence on the Softberry Inc. ...
ReseJ. Antimicrob. Chemother.
(2013) 68 (7): 1543-1550.
doi: 10.1093/jac/dkt078arch
Association of the novel aminoglycoside resistance determinant RmtF with NDM carbapenemase in Enterobacteriaceae isolated in India and the UK
Hidalgo et al.,
1Department of Animal Health and VISAVET, Universidad Complutense de Madrid, Madrid, Spain
2Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Health Protection Agency Microbiology Services – Colindale, London, UK
... into DH5? cells, which were then plated on agar containing ampicillin (50 mg/L) and gentamicin
(10 mg/L). A CloneJET PCR cloning kit (Fermentas International Inc.) was used to clone rmtF
along with its promoter region, previously determined with the Softberry online tool. ...
Plant Physiology and Biochemistry
Volume 69, August 2013, Pages 1–8 DOI:10.1016/j.plaphy.2013.04.007
Fad7 gene identification and fatty acids phenotypic variation in an olive collection by EcoTILLING and sequencing approaches
Sabetta et al.,
a Department of Soil, Plant and Food Sciences, Section of Genetics and Breeding, University of Bari «Aldo Moro», via Amendola 165/A, 70126 Bari, Italy
b CRA-OLI The Olive Growing and Olive Product Industry Research Centre, Contrada LiRocchi, 87036 Rende, Cosenza, Italy
c Department of Crop Systems, Forestry and Environmental Sciences, University of Basilicata, via N. Sauro 85, 85100 Potenza, Italy
... 4.3. EcoTILLING and PCR sequencing. The full-length genomic sequence was analysed
by CODDLE (http://www.proweb.org/input/) and SoftBerry (http://linux1.softberry.com/
berry.phtml) software and the gene structure was predicted. ...
J. Integr. Plant Biol.
Volume 55, Issue 5, pages 462–472, May 2013 doi: 10.1111/jipb.12027
Fine mapping of RppP25, a southern rust resistance gene in maize.
Zhao et al.,
1National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (Ministry of Agriculture), China Agricultural University, Beijing 100193, China
2National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 10081, China
... Prediction of candidate gene The gene structure prediction program SoftBerry (http://linux1.softberry.
com/berry.phtml) and the GENSCAN Web Server at MIT (http://genes.mit.edu/GENSCAN.html)
were used to predict candidate gene in the resistance gene region. ...
J Bone Miner Res,
28: 1041–1049. doi: 10.1002/jbmr.1849
SNX10 mutations define a subgroup of human autosomal recessive osteopetrosis with variable clinical severity
Pangrazio et al.,
1Unita Organizzativa di Supporto/Istituto di Ricerca Genetica e Biomedica, Milan Unit, CNR, Milano, Italy
2Humanitas Clinical and Research Center, Rozzano, Italy
3Division of Immunology, Department of Pediatrics, University of Gothenburg, Gothenburg, Sweden
... the UCSF Chimera package. PovRay was used to generate high-quality images.
The effect of the mutation c.111 + 5G > C was tested using the software
www.fruitfly.org, www.cbs.dtu.dk, and www.linux1.softberry.com. Results. ...
Antibiotics
2013, 2(1), 11-27; doi:10.3390/antibiotics2010011
The Staphylococcus aureus Membrane Protein SA2056 Interacts with Peptidoglycan Synthesis Enzymes
Quiblier et al.,
1 Institute of Medical Microbiology, University of Zurich / Gloriastrasse 32, 8006 Zurich, Switzerland
2 Centre of Quality Control in Microbiology / ul. Chelmska 30/34, 00-725 Warsaw, Poland
... downstream of both femX and sa2056 [15]. Apart from the promoter upstream of femX,
the program softberry identified an additional putative promoter in the intergenic region
between femX and sa2056 [16]. Microarray analyses ...
Advance Journal of Food Science & Technology
2013, Vol. 5 Issue 4, p440-444. 5p.
Cloning of Formate dehydrogenase Gene and Effect on the Waterlogging Tolerance of Brassica napus L
Xu et al.,
... 442 expasy. org and http://www.softberry.com/ berry. phtml). Evaluation of waterlogging
tolerance of 12 materials: One-hundred seeds were submerged in 10 mL of deionized water
in tubes for 24 h in an incubator at 20°C (Ueno and Takahashi, 1997). ...
HAYATI Journal of Biosciences
Vol 20, No 3 (2013)
The Expression of Genes Encoding Secreted Proteins in Medicago truncatula A17 Inoculated Roots
LUCIA KUSUMAWATI, KATHRYN KURAN, NIJAT IMIN, ULRIKE MATHESIUS, MICHAEL DJORDJEVIC
... The open reading frame from Softberry was blasted to the University of Oklahoma Medicago
truncatula genome blast server (http://www.genome.ou.edu/medicago_ blast.html) using blastn
to get the contig number (for example mtgsp_008f03.Contig1 for FAD). ...
Applied Microbiology and Biotechnology
Volume 97, Issue 5 , pp 1941-1952 DOI:10.1007/s00253-012-4044-x
Characterization of a S-layer protein from Lactobacillus crispatus K313 and the domains responsible for binding to cell wall and adherence to collagen
Sun et al.,
1. State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People’s Republic of China
2. Scientific Research Center, Tsingtao Brewery Co.LTD, Qingdao, People’s Republic of China
... Predictions of the open-reading frames (ORF), prokaryotic promoters, and terminators were
performed at http://opal.biology.gatech.edu/ GeneMark/gmhmm2_prok.cgi and http://www.softberry.
com/ berry.phtml. Transcription analysis of the S-layer proteins by qRT-PCR ...
Biology of Reproduction
89(4):Article 98, 1-11. 2013 doi: http://dx.doi.org/10.1095/biolreprod.113.111849
Expression, Regulation, and Promoter Activation of Vanin-2 (VNN2) in Bovine Follicles Prior to Ovulation
Khampoun Sayasith 2, Jean Sirois , and Jacques G. Lussier
Centre de recherche en reproduction animale and the departement de biomedicine veterinaire, Faculte de medecine veterinaire, Universite de Montreal, Saint-Hyacinthe, Quebec, Canada
2Correspondence: Khampoun Sayasith, Centre de recherche en reproduction animale and the departement de biomedecine veterinaire, Faculte de medecine veterinaire, Universite de Montreal, Saint-Hyacinthe, Quebec, Canada
... The promoter sequence was analyzed to identify consensus cis-acting elements (TFSEARCH:
TRANS FAC databases [release date December 1999 and previously hosted at
http://motif.genome.jp/]; Transfac DB, Biobase GmbH [http://linux1.softberry.com/berry.phtml], ...
Fungal Genetics and Biology
Volume 61, December 2013, Pages 69–79 DOI:10.1016/j.fgb.2013.10.006
Disruption of the nitrogen regulatory gene AcareA in Acremonium chrysogenum leads to reduction of cephalosporin production and repression of nitrogen metabolism
Jinyang Li a, b, 1, Yuanyuan Pan a, 1, Gang Liu a
a State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
b University of Chinese Academy of Sciences, Beijing 100049, China
... The insert in the resulting plasmid was verified by sequencing. To confirm AcareA, the
large fragment containing speculated AcareA was analyzed by software softberry. 2.4.
Disruption, complementation and overexpression of AcareA. ...
PloS one
November 13, 2013DOI: 10.1371/journal.pone.0079036
Identification and Molecular Characterization of FKF1 and GI Homologous Genes in Soybean
Li 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, Haidian District, Beijing, China
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, China
... three GI homologs were determined based on further analysis in Softberry database (http://www.softberry.com/berry.phtml). ...
Molecular Biology Reports
Volume 40, Issue 10 , pp 5907-5912 DOI:10.1007/s11033-013-2697-x
Construction and application of the vectors to identify genes encoding exported proteins of Escherichia coli
Niu et al.,
1. College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
2. Veterinary Bureau of Yuhang District, Hangzhou, 311100, China
... gorf/, http://bioinformatics.biol.rug.nl/websoftware/orf/orf_start.php), signal peptide prediction
(http://www.cbs.dtu.dk/services/SignalP/) and promoter analysis tools (http://www.fruitfly.org/
seq_tools/promoter.html, http://molbiol-tools.ca/promscan/, http://linux1.softberry.com/berry ...
Microbiological Research
Volume 168, Issue 8, 1 October 2013, Pages 477–484 DOI:10.1016/j.micres.2013.04.002
A serine hydroxymethyltransferase from marine bacterium Shewanella algae: Isolation, purification, characterization and l-serine production
Wei Jiang, Bingzhao Xia, Ziduo Liu
State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
... A fragment sequence (722 bp) was obtained by PCR with degenerate primers, DP-F and
DP-R. Then through TAIL-PCR, sequences matching and executing the ORF-finding program
on DNA sequence (http://linux1.softberry.com/berry.phtml), the full-length sequence of the ...
Applied Microbiology and Biotechnology
Volume 97, Issue 11 , pp 4965-4976 DOI:10.1007/s00253-013-4851-8
ku70 and ku80 null mutants improve the gene targeting frequency in Monascus ruber M7
Yi He, Qingpei Liu, Yanchun Shao, Fusheng Chen
3. College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People’s Republic of China
1. National Key Laboratory of Agro-Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People’s Republic of China
... Sequence prediction (http://linuxl.softberry.com/berry.phtml) of these two frag- ments revealed
that the putative M. ruber M7 ku70 gene consists of a 1,905-nt long open reading frame (ORF)
interrupted by five introns and the putative M. ruber M7 ku80 gene consists of a 1,998-nt ...
The Journal of Neuroscience
28 August 2013, 33(35): 14087-14097; doi: 10.1523/JNEUROSCI.2710-13.2013
Small-Fiber Neuropathy Nav1.8 Mutation Shifts Activation to Hyperpolarized Potentials and Increases Excitability of Dorsal Root Ganglion Neurons
Huang et al.,
1Department of Neurology and
2Center for Neuroscience and Regeneration Research, Yale University School of Medicine, New Haven, Connecticut 06510,
... Polyphen-2, and Sift characterize the substitution as “c25, likely to interfere with function,” “possibly
damaging,” and “nontolerated.” Splice prediction programs (SpliceSiteFinder, MaxEntScan,
NNSplice, GeneSplicer, Human Splicing Finder, Fruitfly, and Softberry) predict that ...
3 Biotech
September 2013, DOI:10.1007/s13205-013-0164-y
Siderophore biosynthesis genes of Rhizobium sp. isolated from Cicer arietinum L.
Bejoysekhar Datta, Pran K. Chakrabartty
1. Department of Botany, University of Kalyani, Nadia, Kalyani, West Bengal, 741 235, India
2. Acharya J.C. Bose Biotechnology Innovation Centre, Madhyamgram Experimental Farm, Madhyamgram, Kolkata, West Bengal, 700 129, India
... an operon. In the sequence of 4,921 bp, a probable ribosome-binding site (AGGAGG)
was identified six bp upstream of the ATG start codon of sidC of BICC 651 using Promoter
prediction search tool (www.softberry.com). A presumable ...
BMC Genetics
2013, 14:51 doi:10.1186/1471-2156-14-51
Linking the potato genome to the conserved ortholog set (COS) markers
Lindqvist-Kreuze et al.,
1 International Potato Center, Lima, Peru
2 USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin, Madison, WI, USA
... genome sequence, but no gene hit. We ran those genome regions through Softberry
gene prediction and were able to identify genes matching the COS marker hit region
(results not shown). Further work focusing on the genome ...
Molecular Plant-Microbe Interactions
(2013). 26(6), 676-685. DOI:
A Rhamnose-Rich O-Antigen Mediates Adhesion, Virulence, and Host Colonization for the Xylem-Limited Phytopathogen Xylella fastidiosa
Clifford, J. C., Rapicavoli, J. N., & Roper, M. C.
Department of Plant Pathology and Microbiology, University of California, Riverside 92512, U.S.A.
... Online tools used for DNA manipulation and DNA and protein analysis were Integrated Microbial
Genomes, the National Center for Biotechnology Information, San Diego Supercomputer Center
Biology Workbench, Netprimer, and SoftBerry. Mutagenesis and complementation. ...
Journal of bacteriology
(2013). 195(4), 896-907. DOI:10.1128/JB.01973-12
Identification of the Treponema pallidum subsp. pallidum TP0092 (RpoE) Regulon and Its Implications for Pathogen Persistence in the Host and Syphilis Pathogenesis
Giacani, L., Denisenko, O., Tompa, M., & Centurion-Lara, A.
aDepartments of Medicine
bComputer Science and Engineering, University of Washington, Seattle, Washington, USA
...Transcription unit prediction (using http://linux1.softberry.com), hydropathy plot analysis (using http://web.expasy.org/protscale/), and prediction of transmembrane regions (using http://www.ch.embnet.org/software/TMPRED_form.html) identified TP0093 as the best putative anti-? factor for TP0092....
Journal of Invertebrate Pathology
Volume 110, Issue 1, May 2012, Pages 24?32, DOI: 10.1016/j.jip.2012.01.008
The lipopolysaccharide biosynthesis core of the Mexican pathogenic strain Serratia entomophila is associated with toxicity to larvae of Phyllophagablanchardi
Zitlhally Rodriguez-Segura b, Jianwu Chen c, Francisco J. Villalobos d, Sarjeet Gill c, Maria Eugenia Nunez-Valdez a
a Facultad de Ciencias, Universidad Autonoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, CP 62209, Cuernavaca, Morelos, Mexico
b Centro de Investigacion en Biotecnologia, Universidad Autonoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, CP 62209, Cuernavaca, Morelos, Mexico
... Automated sequencing was performed at the University of California Riverside Core
Instrumentation Facility. DNA sequences were analyzed by the Softberry Inc. software. ...
According to the DNA sequence analysis done by using the Softberry, Inc. ...
Journal of Bone and Mineral Research
DOI: 10.1002/jbmr.1849
SNX10 mutations define a subgroup of human Autosomal Recessive Osteopetrosis with variable clinical severity
Pangrazio et al.,
1UOS/IRGB, Milan Unit, CNR, Milano, Italy
2Humanitas Clinical and Research Center, Rozzano, Italy
... Chimera package. PovRay was used to generate high quality images. The effect of
the mutation c.111+5G>C was tested using the software www.fruitfly.org,
www.cbs.dtu.dk and www.linux1.softberry.com. Results Genetic findings ...
Journal of Integrative Agriculture
Volume 11, Issue 10, October 2012, Pages 1592–1600 DOI: 10.1016/S2095-3119(12)60162-2
Isolating the Mutator Transposable Element Insertional Mutant Gene mio16 of Maize Using Double Selected Amplification of Insertion Flanking Fragments (DSAIFF)
ZHONG et al.,
a National Key Laboratory of Crop Genetic Improvement/Huazhong Agricultural University, Wuhan 430070, P.R. China
b Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences/Guizhou Center of Maize Engineering Techniques, Guizhou 550006, P.R. China
... The alignment between the genomic sequence and the cDNA showed that the Mio16
gene contained a 2 550-bp ORF encod- ing a putative 850 aa protein (http://www.
softberry. com), which was composed of 11 exons and 10 introns. ...
PLoS ONE
7(5): e37611. doi:10.1371/journal.pone.0037611
A Unique Regulator Contributes to Quorum Sensing and Virulence in Burkholderia cenocepacia
O'Grady EP, Viteri DF, Sokol PA
Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
... 1). BCAM1871 expression appeared to be driven from the cepI promoter as no other
promoter was identified upstream of the BCAM1871 ORF using promoter prediction
software (www.softberry.com or http://www.fruitfly.org, data not shown). ...
Advanced Science Letters
(2012) Volume 10, Number 1, pp. 153-157(5) DOI: 10.1166/asl.2012.3745
Isolation and Characterization of An Aldo-Keto Reductase cDNA from Camellia Oleifera Seed
Shao, Gongfeng; Tan, Xiaofeng; Chen, Hongpeng,
Laboratory
...Second Structure Analysis and 3D Structure Prediction The Softberry Platform figured out that -helix and -sheet were the main components in the second structure of Co-AKR ..
Advanced Science Letters
(2012) Volume 10, Number 1, pp. 168-172(5) DOI: 10.1166/asl.2012.3722
A Novel Metallothionein Gene Putatively Related to Fatty Acid Biosynthesis in Camellia Oleifera Seeds Confronted to Heavy Metal Stress.
Zhu, Fengyun; Tan, Xiaofeng; Chen, Hongpeng
...The sub-cellular location result predicted by Softberry revealed Co-MT deposit in cytoplasmid and it was a secreted protein. ...
mBio
3(3):e00035-12. doi:10.1128/mBio.00035-12.
Nontypeable Pneumococci Can Be Divided into Multiple cps Types, Including One Type Expressing the Novel Gene pspK
In Ho Park et al.,
Department of Pathology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USAa;
Department of Pediatrics, School of Medicine, Ewha Womans University, Seoul, South Korea
...Insertional sequences and the open reading frames (ORFs) in the DNA sequences were identified using a BLAST search at the National Center for Biotechnology Information website (http://www.ncbi.nlm.nih.gov/BLAST), Softberry (http://www.softberry.com) free web-based software,...
J Mol Endocrinol
April 1, 2012 48 89-97 DOI: 10.1530/JME-11-0105
17b-Estradiol regulates cyclin A1 and cyclin B1 gene expression in adult rat seminiferous tubules
Camille Bois 1,2, Christelle Delalande 1,2, Helene Bouraima-Lelong 1,2, Philippe Durand 3 and Serge Carreau 1,2
1Universite de Caen Basse Normandie,
EA 2608, Laboratoire «Estrogenes et Reproduction», Esplanade de la Paix, F-14032 Caen Cedex, France
2INRA USC 2006,
F-14032 Caen, France
... al. 1990). Promoter regions of cyclin A1 and cyclin B1 gene were analyzed using
TF Search and Softberry online software. The threshold was fixed at 0.85. Terminal
dUDP transferase nick end labeling. Squash preparations ...
Applied Microbiology and Biotechnology
April 2012 DOI: 10.1007/s00253-012-4044-x
Characterization of a S-layer protein from Lactobacillus crispatus K313 and the domains responsible for binding to cell wall and adherence to collagen
Zhilan Sun et al.,
1. State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People’s Republic of China
2. Scientific Research Center, Tsingtao Brewery Co.LTD, Qingdao, People’s Republic of China
... Predictions of the open-reading frames (ORF), prokaryotic promoters, and terminators were
performed at http://opal.biology.gatech.edu/ GeneMark/gmhmm2_prok.cgi and http://www.softberry.
com/ berry.phtml. Transcription analysis of the S-layer proteins by qRT-PCR ...
Journal of Integrative Agriculture
Volume 11, Issue 6, June 2012, Pages 898–909 DOI: 10.1016/S2095-3119(12)60080-X,
Cloning and Characterization of a Somatic Embryogenesis Receptor-Like Kinase Gene in Cotton (Gossypium hirsutum)
Ya-li SHI*,
Rui ZHANG*,
Xiao-ping WU,
Zhi-gang MENG,
San-dui GUO
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
... The full- length cDNA sequence was obtained by primers GS1- 5PF and GS1-3PR (Table
2). Sequence analysis The full-length genomic sequence obtained was analyzed using
the Softberry program (http://linux1.softberry.com/ berry.phtml). ...
American Journal of Molecular Biology
2012 Volume 2, Issue 2 , pp 132-139
Molecular cloning and characterization of fruit specific promoter from Cucumis sativus L.
Sindhu Chandrika Unni ; Padmanabhan Jayanthikumari Vivek ; Thakidiyil Thankappan Maju ; Rintu Thundiyil Varghese ; Eppurathumana Vasudevan Soniya
... promoter for successful fruit specific expression and this region was amplified using PRF and
PRR primers (Figure 1(e)). The 1.5 kb promoter region along with the 5' region of expansin gene
was shown in Figure 2. Transcription start site was predicted using Softberry online tool ...
Genetica
Volume 140, Issue 7-9 , pp 337-347 DOI: 10.1007/s10709-012-9685-2
Characterization of an Ac transposon system based on apt1-m1 (Ac) on the long arm of maize chromosome 9
Fei Wang et al.,
1. School of Life Sciences, Shanghai Key Laboratory of Bio-energy Crop, Shanghai University, 333 Nanchen Road, Shanghai, 200444, People’s Republic of China
... analysis. If the tr-Ac/Ds inserted into a gene, the gene structure could be identified
based on annotations in maizesequence (www.maizesequence.org) and prediction
using gene-finding tools for Eukaryota (www.softberry.com). ...
AEM
Published ahead of print 24 August 2012, DOI: 10.1128/AEM.02065-12
Unveiling the expression characteristics of IspC, a cell wall-associated peptidoglycan hydrolase in Listeria monocytogenes during growth under stress conditions
Jennifer Ronholm 1,2, Xudong Cao 3 and Min Lin 1,2
1Canadian Food Inspection Agency, Ottawa Laboratory Fallowfield, Ottawa, Ontario K2H 8P9, Canada
2Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
... Corresponding to this experimentally determined TSS, there are 209 -10 (TGGTAAAAT) and
-35 (TTGTTA) elements spaced by 19bp, as predicted by a bacterial 210 promoter program
(http://linux1.softberry.com) (Fig. 1). Examination of the sequence in this 211 ...
Theoretical and Applied Genetics
Volume 125, Issue 8 , pp 1717-1726 DOI: 10.1007/s00122-012-1948-x
Mapping and characterization of the major quantitative trait locus qSS7 associated with increased length and decreased width of rice seeds
Xianjin Qiu, Rong Gong, Youbin Tan, Sibin Yu
1. National Key Laboratory of Crop Genetic Improvement, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
... The 23-kb target region contains two common predicted genes (LOC_Os07g41200,
LOC_Os07g41210) based on three genome annotation databases (http://rice.plantbiology.
msu.edu/; http://ricegaas.dna.affrc.go.jp/; http://linux1.softberry.com/) (Fig. ...
Viruses.
2012 April; 4(4): 581–612.
Published online 2012 April 16. doi: 10.3390/v4040581
RNA-Sequencing Analysis of 5' Capped RNAs Identifies Many New Differentially Expressed Genes in Acute Hepatitis C Virus Infection
Papic et al.,
1 Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA
2 Huntsman Cancer Institute, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA
...Using the ORF Finder software (Softberry) we found a small peptide of 48 amino acids encoded in this unannotated transcript ...
Insect Molecular Biology
Volume 21, Issue 4, pages 395–404, August 2012 DOI: 10.1111/j.1365-2583.2012.01145.x
Physiological significance of alternatively spliced exon combinations of the single-copy gene class A chitin synthase in the insect Ostrinia furnacalis (Lepidoptera)
M. Qu, Q. Yang
School of Bioscience and Biotechnology, Dalian University of Technology, Dalian, China
... DNA and protein sequence analyses. DNA sequence data for OfCHSA (GenBank ID: EU376026)
were translated to amino acids by DNAMAN software (Lynnon, Quebec, Canada). The splicing
sites of OfCHSA were analysed with SoftBerry (http://www.softberry.com/all.htm). ...
Front Plant Sci.
2012; 3: 54. DOI: 10.3389/fpls.2012.00054
Turnover of Phosphatidic Acid through Distinct Signaling Pathways Affects Multiple Aspects of Pollen Tube Growth in Tobacco
Pleskot et al.,
1Institute of Experimental Botany, v. v. i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
2Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
... Since gene models based on computer annotations often contain errors, exon-intron structures were
manually curated using SoftBerry server4 with the aid of experimentally verified
sequences or sequences from closely related species. ...
Molecular Microbiology
Volume 86, Issue 2, pages 394–410, October 2012
DOI: 10.1111/j.1365-2958.2012.08203.x
sarA negatively regulates Staphylococcus epidermidis biofilm formation by modulating expression of 1 MDa extracellular matrix binding protein and autolysis-dependent release of eDNA
Christner et al.,
1Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
2Institute for Clinical Chemistry, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
... Bioinformatics analysis of 150 nucleotides up-stream of the embp start codon identified three
high affinity SarA binding sites as defined by Sterba and co-workers (Sterba et al., 2003), two
located near or within the anticipated ?10 region (http://linux1.softberry.com), suggesting ...
J. Virol.
November 2012 vol. 86 no. 21 11937-11938 doi: 10.1128/?JVI.02009-12
Complete Genome Sequence of a J Subgroup Avian Leukosis Virus Isolated from Local Commercial Broilers
Hongxin Li et al.,
a College of Animal Science, South China Agricultural University, Guangzhou, China
... Japan), sequenced three times, and assembled using DNAStar (version 7). Multiple-sequence
alignment was performed with Clustal X (BioEdit version 7). The transcriptional regulatory
elements in noncoding regions of the genome were analyzed with SoftBerry (Softberry, Inc ...
Journal of Biotech Research
[ISSN: 1944-3285] 2012; 4:54-64
Acetogen biocatalyst Clostridium sp. MTEtOH871 engineered with our proprietary electrotransformation technology and equipment: continuous synthesis gas fermentation for selective ethanol production
Vel Berzin and Michael Tyurin*
Syngas Biofuels Energy, Inc., 2441 Del Monte, Houston, TX 77019, USA.
... Promoter and terminator sequences were identified using Softberry Bacterial Promoter, Operon
and Gene finding tool (http://linux1.softberry.com/). We used the origin of replication of a
~35-copy number 1.8 kb cryptic plasmid pMT351 we have isolated previously from the ...
J. Virol.
doi: 10.1128/?JVI.01894-12 October 2012 vol. 86 no. 19 10907-10908
Complete Genome Sequence of an Avian Leukosis Virus Isolate Associated with Hemangioma and Myeloid Leukosis in Egg-Type and Meat-Type Chickens
Jun Ji et al.,
aCollege of Animal Science, South China Agricultural University, Guangzhou, China
bCollege of Veterinary Medicine, South China Agricultural University, Guangzhou, China
... Multiple-sequence alignment was performed with Clustal X (BioEdit version 7). The
transcriptional regulatory elements in noncoding regions of the genome were analyzed
with SoftBerry (Softberry, Inc., Mount Kisco, NY). Comparative ...
Molecular Biology Reports
July 2012, Volume 39, Issue 7, pp 7347-7353 DOI
10.1007/s11033-012-1566-3
Assay and characterization of an osmolarity inducible promoter newly isolated from Bacillus subtilis
Wei-Wei Zhang (1)
Qiu-Rong Gao (1)
Ming-Ming Yang (2)
Hui Liu (2)
Dun Wang (1)
1. College of Life Sciences, Northwest A&F University, Yangling, 712100, People’s Republic of China
2. College of Animal Sciences, Yangling, 712100, People’s Republic of China
... Analysis of DNA sequence of the pro- moter-active fragment was carried out online with NCBI
blast 2.0 (http: www.ncbi.nih.gov). The promoter was predicted by softberry (http:
www.softberry.com). Results and discussion Characterization of an osmolarity-inducible promoter ...
Journal of Plant Physiology
Volume 169, Issue 11, 15 July 2012, Pages 1112–1120
Molecular characterization of two ethylene response factor genes in sweetpotato that respond to stress and activate the expression of defense genes in tobacco leaves
Yun-Hee Kima, 1,
Jae Cheol Jeonga, 1,
Seyeon Parka, b,
Haeng-Soon Leea, b,
Sang-Soo Kwaka, b,
a Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 305-806, Republic of Korea
b Green Chemistry and Environmental Biotechnology, University of Science and Technology (UST), 217 Gajungro, Yuseong-gu, Daejeon 305-350, Republic of Korea
... To predict the isoelectric point (pI), molecular weight and signal peptides of the deduced proteins,
the ExPasy (http://www.expasy.org/tools), PSORT (http://psort.ims.u-tokyo.ac.jp) and SoftBerry
(http://www.softberry.com) programs were used. Subcellular localization of ERFs. ...
African Journal of Biotechnology
Vol. 11 (29), pp. 7378-7387, 10 April, 2012
DOI: 10.5897/AJB11.2875
Isolating Barley (Hordeum vulgare L.) B1 Hordein Gene Promoter and Using Sequencing Analaysis For The Identification of Conserved Regulatory Elements By Bioinformatic Tools
Kobra Nalbandi1, Bahram Baghban Kohnehrouz2* , Khalil Alami Saeed1 and Ashraf Gholizadeh3
1Ramin Agricultural and Natural Resources University, Mollasani, Ahwaz, Iran.
2Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, Iran.
3Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran.
... Hor.W. To find regulatory elements in promoter sequences, the PLANTCARE
(http://bioinformatics.psb.ugent.be/ webtools/plantcare/html) and Softberry
(http://linux1.softberry.com/berry.phtml) software were applied. Analysis ...
Polar Biology
October 2012, Volume 35, Issue 10, pp 1515-1524 DOI
10.1007/s00300-012-1191-6
Characterization and expression analysis of three cold shock protein (CSP) genes under different stress conditions in the Antarctic bacterium Psychrobacter sp. G
Weizhi Song (1) (2)
Xuezheng Lin (1) (2)
Xiaohang Huang (1) (2)
1. First Institute of Oceanography, SOA, Qingdao, 266061, China
2. Key Lab of Marine Bioactive Substances, SOA, Qingdao, 266061, China
... The regulatory sequences (ie, -10 region, -35 region, ribosomal binding site (RBS), DB, and
ORF) were analyzed using the Softberry (http:// linux1.softberry.com/berry.phtml) (Panicker
et al. 2010) and Neural Network Promoter Prediction (http://www. ...
Advanced Science Letters
Volume 10, Number 1, May 2012 , pp. 146-152(7) DOI: http://dx.doi.org/10.1166/asl.2012.3743
Cloning and Bioinformatics Analysis of a Peroxidase Gene from Camellia Oleifera Seed
Chen, Hongpeng; Tan, Xiaofeng; Shao, Gongfeng
... and chemical property of predicted protein, genetic evo- lution, homology modeling, 3D structural
optimization and ren- dering were analyzed with Codon W, Antheprot 5.0, Clustral X,
SWISS-MODEL sever, VMD1.8.5 and POV-Ray respectively, NCBI center, Softberry platform ...
Gene.
2012 Oct 1;507(1):9-19. Epub 2012 Jul 24.
BnC15 and BnATA20, the different putative components, control anther development in Brassica napus L.
Wan L, Hu Q, Hong D, Yang G.
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, PR China.
... downstream of the coding sequence. Full cDNA sequence was analyzed using
Softberry (http://linuxl.softberry.com/berry.phtml) and GeneScan Web Server
(http://genes.mit.edu/- GENSCAN.html). The deduced protein was viewed ...
Molecular Breeding
Volume 29, Issue 4 , pp 939-949 DOI
10.1007/s11032-011-9644-0
Validation of DGAT1-2 polymorphisms associated with oil content and development of functional markers for molecular breeding of high-oil maize
Yuchao Chai et al.,
1. National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
2. Pioneer Hi-Bred International Inc., Johnston, IA, 50131–1004, USA
... 2008) was used to BLAST against the maize high-throughput genomic sequences database
(www.ncbi.nlm.nih.gov) to obtain the B73 genomic sequence. The gene structure was predicted
using online tools from the Softberry web site (www.softberry.com). ...
Animal Biotechnology
Volume 23, Issue 3, 2012 pages 156-173 DOI:10.1080/10495398.2012.662925
Screening of a Xylanase Clone from a Fosmid Library of Rumen Microbiota in Hu Sheep
Dr. Jiakun Wang et al.,
a College of Animal Sciences, Zhejiang University, Hangzhou, China
b Center for Biomedicine and health, Hangzhou Normal University, Hangzhou, China
... The GC composition was studied using the DNAStar software. Open reading frames (ORFs) were
characterized using Softberry online program using the criteria of sequences encoding peptides
longer than 50 amino acids (http://linux1.softberry.com/berry.phtml). ...
Letters in Applied Microbiology
Volume 55, Issue 2, pages 149–154, August 2012 DOI: 10.1111/j.1472-765X.2012.03272.x
Selective production of acetone during continuous synthesis gas fermentation by engineered biocatalyst Clostridium sp. MAceT113
V. Berzin1, M. Kiriukhin2, M. Tyurin1
1 ?Syngas Biofuels Energy, Inc., Houston, TX, USA
2 Ajinomoto – Genetika Research Institute, Moscow, Russia
... ljungdahliiDSM13528 (NC_014328, region 1295679…1297232, nucleotides 1–564). Promoter
and terminator sequences used in both vectors were identified using Softberry Bacterial
Promoter, Operon and Gene Finding tool (http://linux1.softberry.com/). ...
International Journal of Medical Microbiology
Volume 302, Issue 3, July 2012, Pages 117–128 http://dx.doi.org/10.1016/j.ijmm.2012.03.003
Surface-associated motility, a common trait of clinical isolates of Acinetobacter baumannii, depends on 1,3-diaminopropane
Evelyn Skiebe et al.,
a Robert Koch-Institute, Wernigerode Branch, D-38855 Wernigerode, Germany
b CEA, DSV, IG, Genoscope, 2 rue Gaston Cremieux, 91057 Evry, France
... A 3815-bp fragment encompassing genes A1S-2453 (ddc) and A1S-2454 (dat) as well as the
putative promoter and terminator regions (analysed with the softberry package available online:
http://linux1.softberry.com/berry.phtml) was amplified by PCR (see Fig. ...
Applied Biochemistry and Biotechnology
Volume 167, Issue 2 , pp 338-347 DOI
10.1007/s12010-012-9697-5
Elimination of Acetate Production to Improve Ethanol Yield During Continuous Synthesis Gas Fermentation by Engineered Biocatalyst Clostridium sp. MTEtOH550
Vel Berzin (1)
Michael Kiriukhin (2)
Michael Tyurin (1)
1. Syngas Biofuels Energy, Inc., 2441 Del Monte, Houston, TX, 77019, USA
2. Ajinomoto-Genetika Research Institute, 1st Dorozhny pr. 1-1, Moscow, Russia, 117545
... 2627526) flanking cat gene (FM201786) CDS. Promoter and terminator sequen-
ces were identified using Softberry Bacterial Promoter, Operon and Gene finding
tool (http:// linux1.softberry.com/). Detection of synthetic cat was ...
Gene
Volume 498, Issue 2, 1 May 2012, Pages 280–287
DNA adenine methyltransferase (Dam) controls the expression of the cytotoxic enterotoxin (act) gene of Aeromonas hydrophila via tRNA modifying enzyme-glucose-inhibited division protein (GidA)
Tatiana E. Erova a,
Valeri G. Kosykh b,
Jian Sha a,
Ashok K. Chopra a
a Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555-1070, USA
b Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-1070, USA
... vector (Invitrogen, Carlsbad, CA). Upstream sequences of the gidA and act genes
of A. hydrophila SSU contained promoter regions, which we identified by using the
SoftBerry program (www.softberry.com). To obtain PCR products ...
Mol. Plant
(2012) 5 (5): 1042-1057. doi: 10.1093/mp/sss003
The Arabidopsis AP2/ERF Transcription Factor RAP2.11 Modulates Plant Response to Low-Potassium Conditions
Min Jung Kima,
Daniel Ruzickaa,
Ryoung Shinb and
Daniel P. Schachtmana,c,1
aDonald Danforth Plant Science Center, St Louis, MO 63132, USA
bRIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan
... (A) AtHAK5 promoter contains ERE, CGTCA (MeJA responsiveness), ABRE (ABA
responsiveness), GCC-box, and CE3 (ABA responsiveness) elements. SoftBerry
(www.softberry.com/berry.phtml) was used as a promoter prediction tool. ...
Journal of Biotech Research
2012; 4:1-12
Electrofusion of cells of Acetogen Clostridium sp. MT 351 with erm(B) or cat in the chromosome
Michael Tyurin 1, *, Michael Kiriukhin 2, Vel Berzin 1
1Syngas Biofuels Energy, Inc., 2441 Del Monte, Houston, TX 77019, USA. 2Ajinomoto Company, 1st Dorozny pr. 1-1, Moscow, Russia 117545
... downstream of erm(B) (AY334073), respectively. Promoter and terminator sequences
were identified using Softberry Bacterial Promoter, Operon and Gene Finding tool
(http://linux1.softberry.com/). The resulted synthetic ermB operon ...
Theoretical and Applied Genetics
August 2012 DOI
10.1007/s00122-012-1954-z
QTL mapping of resistance to gray leaf spot in maize
Yan Zhang et al.,
1. National Maize Improvement Center of China, China Agricultural University, 2 West Yuanmingyuan Road, Haidian District, Beijing, 100193, People’s Republic of China
2. Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Longtou Street, Kunming, 650205, People’s Republic of China
... In an attempt to find out more InDels, we predicted putative genes in the single-/low- copy
sequence using tools in software SoftBerry (http:// linux1.softberry.com/berry.phtml), and designed
primers in either 50- or 30- ends of the predicted genes as high-level polymorphism is ...
Applied Biochemistry and Biotechnology
September 2012 DOI
10.1007/s12010-012-9864-8
Cre-lox66/lox71-Based Elimination of Phosphotransacetylase or Acetaldehyde Dehydrogenase Shifted Carbon Flux in Acetogen Rendering Selective Overproduction of Ethanol or Acetate
Vel Berzin (1)
Michael Kiriukhin (2)
Michael Tyurin michael@syngasbiofuelsenergy.com (1)
1. Syngas Biofuels Energy, Inc., 2441 Del Monte, Houston, TX, 77019, USA
2. Ajinomoto—Genetika Research Institute, 1st Dorozhny pr. 1-1, Moscow, Russia, 117545
... Inactivation of pta was performed as described [13] using integration vector pMT674pta. Promoter
and terminator sequences used in all integration vectors were identified using Softberry Bacterial
Promoter, Operon, and Gene Finding tool (http://linux1.softberry.com/). PCR ...
The Journal of Immunology
July 15, 2012 vol. 189 no. 2 539-550 doi: 10.4049/jimmunol.1103204
Identification, Cloning, and Functional Characterization of the IL-1 Receptor Antagonist in the Chicken Reveal Important Differences between the Chicken and Mammals
Mark S. Gibson*,
Mark Fife*,
Steve Bird†,
Nigel Salmon* and
Pete Kaiser*,1
*Institute for Animal Health, Compton, Berkshire RG20 7NN, United Kingdom; and
†Department of Biological Sciences, School of Science and Engineering, University of Waikato, Hamilton 3240, New Zealand
... HE608245). Putative promoter regions were analyzed using Softberry (http://linux1.
softberry.com/berry.phtml). 5? RACE was carried out using the SMARTer RACE cDNA
amplification kit (Clontech) following the manufacturer's instructions. ...
Plant Molecular Biology Reporter
August 2012 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)
Ratnam Wickneswari wicki@ukm.my (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 ...
Insect Biochemistry and Molecular Biology
Available online 25 September 2012 http://dx.doi.org/10.1016/j.ibmb.2012.09.006
In Press, Uncorrected Proof — Note to users
Expansion of the silkworm GMC oxidoreductase genes is associated with immunity
Wei Sun a et al.,
a The Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
b College of Life Sciences, Chongqing University, Chongqing 400044, China
... domains. It was hypothesized that either of these two genes could be two single genes.
Indeed, both of them could be divided into two genes when re-analyzed using
Softberry (http://linux1.softberry.com/berry.phtml). Therefore ...
Antimicrob. Agents Chemother.
August 2012 vol. 56 no. 8 4450-4458 doi: 10.1128/?AAC.00456-12
Characterization of RarA, a Novel AraC Family Multidrug Resistance Regulator in Klebsiella pneumoniae
Mark Veleba a
aCentre for Infection and Immunity, Queen's University Belfast, Medical Biology Centre, Belfast, United Kingdom
bInstitute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
... The junction between the C tail and the start site of rarA open reading frame was taken
to be the transcriptional start site. Predictions of the putative ?10 and ?35 hexamers were
determined using SoftBerry analysis of the intergenic region. ...
Cellular Signalling
Volume 25, Issue 1, January 2013, Pages 168–177 http://dx.doi.org/10.1016/j.cellsig.2012.09.006,
Structural diversity of the cAMP-dependent protein kinase regulatory subunit in Caenorhabditis elegans
Martyna W. Pastok et al.,
Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown St., Liverpool, L69 7ZB, United Kingdom
... http://opal.biology.gatech.edu/GeneMark/eukhmm.cgi), Grail (http://compbio.ornl.gov/Grail-1.3/),
GeneScan (http://genes.mit.edu/GENSCAN.html) and GeneFinder (http://www.bioscience.org/
urllists/genefind.htm) together with various tools available from Softberry (http://linux1 ...
MPMI
November 2012, Volume 25, Number 11
Pages 1419-1429
http://dx.doi.org/10.1094/MPMI-06-12-0155-R
A Polyketide Synthase Gene, ACRTS2, Is Responsible for Biosynthesis of Host-Selective ACR-Toxin in the Rough Lemon Pathotype of Alternaria alternata
Y. Izumi et al.,
1Faculty of Agriculture, Kagawa University, Miki, Kagawa 761-0795 Japan; 2Department of Plant Pathology, Washington State University, Pullman 99164-6430 U.S.A.
... with the largest contig at approximately 41 kb. One 17 kb contig (C14014) contained 12 three
open reading frames (ORFs) that encoded two unknown proteins and a putative 13 PKS,
identified via SoftBerry and BLAST/FASTA searches. The putative 14 ...
Human Mutation
Volume 33, Issue 11, pages 1576–1588, November 2012 DOI: 10.1002/humu.22142
Comprehensive functional assessment of MLH1 variants of unknown significance
Ester Borras et al.,
1
Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IDIBELL, Hospitalet de Llobregat, Spain
2
Medical Clinic 1, Johann Wolfgang Goethe-University Clinic, Frankfurt, Germany
... To identify potential splicing mutations, disruption or creation of SS were evaluated
using NNSplice [Reese et al., 1997], Splicerport [Dogan et al., 2007], NetGene2 Server
[Hebsgaard et al., 1996], and SoftBerry [Burset et al., 2001]. ...
Microbial Pathogenesis
Volume 52, Issue 4, April 2012, Pages 227–238 http://dx.doi.org/10.1016/j.micpath.2012.01.004,
The Mycobacterium avium ESX-5 PPE protein, PPE25-MAV, interacts with an ESAT-6 family Protein, MAV_2921, and localizes to the bacterial surface
Michael McNamara a, b,
Lia Danelishvili a,
Luiz E. Bermudez a, b, c
a Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
b Molecular and Cellular Biology Program, College of Science, Oregon State University, Corvallis, OR, USA
... PCR analysis (Suppl. Table 4). Bioinformatics analysis of potential operons and
terminator sites was performed using Softberry software (Softberry, Mount Kisko,
NY). 2.13. Statistical analysis. Each experiment was repeated ...
Extremophiles
Volume 16, Issue 1 , pp 35-43
DOI: 10.1007/s00792-011-0403-2
Effects of salts on activity of halophilic cellulase with glucomannanase activity isolated from alkaliphilic and halophilic Bacillus sp. BG-CS10
Guimin Zhang (1) (2)
Shunyi Li (2)
Yanfen Xue (1)
Liangwei Mao (2)
Yanhe Ma (1)
1. State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
2. College of Life Sciences, Hubei University, Wuhan, 430062, China
... The signal peptide was identified using the SignalP 3.0 server (http:// www.cbs.dtu.dk/
services/SignalP), and the promoter sequence was predicted online (http://linux1.
softberry. com/berry.phtml). Construction of the expression plasmid ...
Appl. Environ. Microbiol.
January 2012 vol. 78 no. 2 581-585 DOI 10.1128/?AEM.06611-11
Controlled Gene Expression in Bifidobacteria by Use of a Bile-Responsive Element
Lorena Ruiz et al.,
Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lacteos de Asturias (IPLA), Consejo Superior de Investigaciones Cientificas (CSIC), Villaviciosa, Asturias, Spain
... Schematic representation of the constructs used in this work. (A) Main features of the betA
upstream region (unpublished data) deduced after the analysis with Softberry and Neural Network
Promoter Prediction. Pin-like symbols represent potential inverted repeats. ...
Scientific Reports
2, Article number: 228 doi:10.1038/srep00228 2012
Recruitment in the sea: bacterial genes required for inducing larval settlement in a polychaete worm
Ying Huang, Sean Callahan & Michael G. Hadfield
... Promoter prediction was performed using the BPROM program, which predicts bacterial promoters and is available through the Softberry website (http://linux1.softberry.com/berry.phtml?topic=index&group=program&subgroup=promoter) ...
Breast Cancer Research and Treatment
Volume 121, Number 1, 177-184, DOI: 10.1007/s10549-009-0532-9
Potentially functional polymorphisms in ESR1 and breast cancer risk: a meta-analysis
Ni Li, Jing Dong, Zhibin Hu, Hongbing Shen and Min Dai
(1) National Office of Cancer Prevention and Control, Cancer Hospital/Institute, Chinese Academy of Medical Sciences, 17 Panjiayuannanli, Chaoyang District, 100021 Beijing, China
(2) Department of Epidemiology and Biostatistics, Cancer Center, Nanjing Medical University, 210029 Nanjing, China
... For SNPs in the promoter region and 50UTR, we use software in the web site of Softberry
(http://www. softberry.com/berry.phtml) and use TF search (http://www. cbrc.jp/research/db/
TFSEARCH.html) to see the change of transcription factor binding. ...
Plant Molecular Biology
DOI: 10.1007/s11103-009-9557-z
OsPRP3, a flower specific proline-rich protein of rice, determines extracellular matrix structure of floral organs and its overexpression confers cold-tolerance
Kodiveri Muthukalianan Gothandam 1 , Easwaran Nalini 1, Sivashanmugam Karthikeyan 1 and Jeong Sheop Shin 2
(1) School of Bio Sciences & Technology, VIT University, Vellore, 632 014, Tamil Nadu, India
(2) School of Life Sciences & Biotechnology, Korea University, Seoul, 136-701, Korea
... 2000). Nucleotide and deduced amino acid sequence were analyzed with the Basic Local Align-
ment Search Tool (BLAST) at the National Center for Biotechnology Information
(http://www.ncbi.nlm.nih.gov) and the Soft berry programme (http://www.softberry.com). ...
Biology of Reproduction
Published online before print March 3, 2010, doi: 10.1095/?biolreprod.109.082644
Kit System in the Zebrafish Ovary--Evidence for Functional Divergence of Two Isoforms of Kit (Kita and Kitb) and Kit Ligands (Kitlga and Kitlgb) During Folliculogenesis
Kai Yao and
Wei Ge
... For kitb, a partial genomic sequence was available in the Ensembl Databank (
ENSDARG00000056133; http://www.ensembl.org/Danio_rerio/) and the exons of kitb were
predicted by CBS PREDICTION SERVERS (http://www.cbs.dtu.dk/services/) and SOFTBERRY ( ...
Molecular Biotechnology
Volume 46, Number 2, 127-133, DOI: 10.1007/s12033-010-9277-2
Novel Expression System for Combined Vaccine Production in Edwardsiella tarda Ghost and Cadaver Cells Novel Expression System for Combined Vaccine Production in Edwardsiella tarda Ghost and Cadaver Cells
Seung Hyuk Choi 1, Yoon Kwon Nam 2 and Ki Hong Kim 1
(1) Department of Aquatic Life Medicine, Pukyong National University, Busan, 608-737, Korea
(2) Department of Aquaculture, Pukyong National University, Busan, 608-737, Korea
... of the trapped fragment. Based on the bioinformatic prediction of putative promoter
region (SOFTBERRY; http://linux1.softberry.com/berry. phtml), a clone (C#28) was
chosen for the trimming of the promoter region. From the C ...
Genetics
Vol. 184, 975-983, April 2010 doi:10.1534/genetics.109.112557
An Interspecific Plant Hybrid Shows Novel Changes in Parental Splice Forms of Genes for Splicing Factors
Moira Scascitelli, Marie Cognet 1 and Keith L. Adams 2
University of British Columbia Botanical Garden and Centre for Plant Research, and Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
... When gene models were not available, we analyzed putative gene exon/intron structures and
protein sequence predictions with gene finding programs from Softberry (http://linux1.softberry.
com/berry.phtml). View this table: In this window In a new window, TABLE 1. ...
Appl. Environ. Microbiol.
doi:10.1128/AEM.01742-10
Ralstonia solanacearum Dps contributes to oxidative stress tolerance, colonization, and virulence on tomato plants
Jennifer M. Colburn-Clifford, Jacob M. Scherf, and Caitilyn Allen
University of Wisconsin-Madison Department of Plant Pathology, 1630 Linden Dr., Madison WI 53706 USA
... Page 6. AEM01742-10 Version 2 -6- as previously described (1). DNA and protein
sequences were analyzed using Softberry 118 (http://linux1.softberry.com/berry.
phtml), Biology Workbench (http://workbench.sdsc.edu/), 119 ...
New Biotechnology
Volume 27, Issue 4, 30 September 2010, Pages 289-299 doi:10.1016/j.nbt.2010.01.337
Isolation and characterization of oil palm constitutive promoter derived from ubiquitin extension protein (uep1) gene
Subhi Siti Masura 1, Ghulam Kadir Ahmad Parveez 1, and Ismanizan Ismail 2
1 Advanced Biotechnology and Breeding Centre (ABBC), Biological Research Division, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720 Kuala Lumpur, Malaysia
2 School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
... assembly. DNA and protein homology searches against GenBank databases were
performed using BLAST 2.0 [23]. Prediction of putative location of transcription start
sites was carried out using the Softberry database. Identification ...
Extremophiles
2010 Mar;14(2):171-83. Epub 2009 Dec 20.
Occurrence and distribution of capB in Antarctic microorganisms and study of its structure and regulation in the Antarctic biodegradative Pseudomonas sp. 30/3
Panicker G, Mojib N, Nakatsuji T, Aislabie J, Bej AK.
Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, CH103, Birmingham, AL, 34294-1170, USA.
... ncbi.nlm.nih.gov) using the Basic Local Alignment Search Tool (BLAST). The promoter,
RBS and ORF sequences were analyzed using Softberry (http://softberry.com/berry.
phtml) and Geneious (http://www.geneious.com) software. ...
Plant Physiology and Biochemistry
Volume 48, Issues 2-3, February-March 2010, Pages 153-159 doi:10.1016/j.plaphy.2009.12.008
Identification of iron-deficiency responsive microRNA genes and cis-elements in Arabidopsis
Wei Wei Kong a and Zhi Min Yang
a Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
... Using transcription start site (TSS) predicted software (SoftBerry, http://www.softberry.com), we
were able to obtain 139 (74.3%) 2 kb proximal promoter sequences upstream of pre-miRNAs.
These sequences contain at least one transcription start site or promoter. ...
Microbial Pathogenesis
Volume 48, Issue 5, May 2010, Pages 168-177 doi:10.1016/j.micpath.2010.02.006
The Burkholderia cenocepacia K56-2 pleiotropic regulator Pbr, is required for stress resistance and virulence
Ramos et al.,
a IBB – Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Instituto Superior Tecnico, Torre Sul, Piso 6. Av. Rovisco Pais, 1049-001 Lisboa, Portugal
b Department of Microbiology, Institute of Plant Biology, University of Zurich, Zurich, Switzerland
... pbr and phzD–phzF (Fig. 1C). These results demonstrate that phzD and phzF are
forming an operon, which was predicted using the Softberry software suite
(http://linux1.softberry.com/berry.phtml). The two fragments could not ...
Planta
DOI: 10.1007/s00425-010-1326-3
Sweetpotato late embryogenesis abundant 14 (IbLEA14) gene influences lignification and increases osmotic- and salt stress-tolerance of transgenic calli
Park et al.,
... http://www.expasy.org/tools), PSORT (http://psort.ims. u-tokyo.ac.jp), and SoftBerry
(http://www.softberry.com) programs. Planta 123 Page 4. Gene expression analysis
Total RNA was isolated from sweetpotato using TRIzol reagent ..
International Journal of Medical Microbiology
Volume 300, Issue 5, June 2010, Pages 279-288
Characterisation of multidrug-resistant Salmonella Typhimurium 4,[5],12:i:- DT193 strains carrying a novel genomic island adjacent to the thrW tRNA locus
Sandra Trupschuch a, 1, Jenny A. Laverde Gomez a, 1, Ia Ediberidze b, Antje Flieger a and Wolfgang Rabsch a
a Division of Bacterial Infections and National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch-Institute, Wernigerode Branch, Germany
b Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi, Georgia
.. For bioinformatical analyses, we used the following online available software tools:
www.ncbi.nlm.nih.gov/ for NCBI's BLASTn and BLASTx analyses; linux1.softberry.com
/berry.phtml for promotor search; www.effectors.org for the prediction of potential T3SS-secreted ...
European journal of plant pathology
2010, vol. 127, no3, pp. 351-363
Alternative splicing and genetic diversity of the white collar-1 (wc-1) gene in cereal Phaeosphaeria pathogens
Ericka et al.,
(1) Seed Improvement and Propagation Station, Taichung 426, TAIWAN, PROVINCE DE CHINE
(2) Department of Plant Pathology, National Chung Hsing University, Taichung City 402, TAIWAN, PROVINCE DE CHINE
... When the wc-1 genomic sequence was analyzed by Softberry (http://linux1.softberry. ...
Therefore, the deduced WC-1 polypep- tide (1,076 aa) analyzed by Softberry was three
amino acids fewer as compared to the analysis from the Broad Institute. ...
PLoS ONE
2010, 5(5): e10803. doi:10.1371/journal.pone.0010803
The Monofunctional Catalase KatE of Xanthomonas axonopodis pv. citri Is Required for Full Virulence in Citrus Plants
Tondo ML, Petrocelli S, Ottado J, Orellano EG
Molecular Biology Division, Facultad de Ciencias Bioquimicas y Farmaceuticas, Instituto de Biologia Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Cientificas y Tecnicas, Universidad Nacional de Rosario, Rosario, Argentina
... bp upstream of the 5? end to 14 bp downstream of the 3? end of the ORF was amplified using
the primer pair ckatE-F and ckatE-R (Table 1). The amplified sequence included the putative
promoter sequence of the katE gene, previously predicted with SoftBerry (www.softberry ...
The Journal of Agricultural Science
2010, 148: 579-591, DOI: 10.1017/S0021859610000420
Gene expression and nitrogen loss in senescing root systems of red clover (Trifolium pratense)
WEBB et al.,
a1 Institute of Biological, Environmental and Rural Sciences, Gogerddan, Aberystwyth, Ceredigion SY23 3EB, UK
a2 Department of Environmental and Geographical Sciences, Manchester Metropolitan University, Manchester M1 5GD, UK
... DNA sequences were aligned using ClustalW. Gene structure was analysed using multiple
alignment construction and analysis workbench (MACAW) and Softberry (Mount KIsco, New York,
USA; http://linux1.softberry.com/berry.phtml). ... Analysis by Softberry shows two exons. ...
Acta Derm Venereol.
2010;90(1):95-6
A new SPINK5 donor splice site mutation in siblings with Netherton syndrome
Tuysuz et al.,
... Page 2. 96 Letters to the Editor using two different software programs available at http://www.
fruitfly.org/ and http://linux1.softberry.com). Both predictors showed that the splice site score of
the mutant sequence was much lower (0.59) than the wild-type counterpart (0.96). ...
African Journal of Biotechnology
Vol. 9(41), pp. 6826-6834, 11 October, 2010
Cloning and functional analysis in transgenic tobacco of a tapetum-specific promoter from Arabidopsis
Xuan-Li Nie, Jian-Wei Zhu, An-Qi Geng and Xing-Guo Xiao
State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
... In order to identify this kind of cis-elements, we analyzed in detail the DNA sequence of the -155
region (Figure 5) with Plant CARE (http://bioinformatics.psb,ugent.be/webtools/plantcare/ht ml)
and SOFTBERRY (http://linuxl.softberry.com/berry. phtml), in addition to PLACE. ...
International Journal of Hydrogen Energy
Volume 35, Issue 3, February 2010, Pages 1065-1073 doi:10.1016/j.ijhydene.2009.11.102
Molecular characterization and homologous overexpression of [FeFe]-hydrogenase in Clostridium tyrobutyricum JM1
Ji Hye Jo a, Che Ok Jeon b, Seung Yoon Lee c, Dae Sung Lee d, and Jong Moon Park e
a Biosciences Center, National Renewable Energy Laboratory, 1617 Cole Blvd, Golden, CO 80401-3393, USA
b Department of Life Science, Chung-Ang University, Seoul 156-756, South Korea
... nucleotide identity. Transcription promoters and termination sequences of the hydA
gene were analyzed using web-based programs (http://www.softberry.com/;
http://www.fruitfly.org/seq.tools/promoters. html). The theoretical ...
Journal of plant biology
2010, vol. 53, no2, pp. 134-141
Cloning and Characterization of Functional Trehalose-6-Phosphate Synthase Gene in Maize
Jiang Wei (1) ; Fu Feng-Ling (1) ; Zhang Su-Zhi (1) ; Wu Ling (1) ; Li Wan-Chen (1)
(1) Maize Research Institute, Sichuan Agricultural University, Sichuan, Ya’an, China
... The completely matched sequence together with its sequences within 5,000 bp upstream and
downstream, a total of 15,000 bp, was used to analyze the gene structure using GeneFinder
software (http://linux1.softberry.com). Open Reading Frame Cloning ...
Antimicrob. Agents Chemother.
doi:10.1128/AAC.01672-09
A novel insertion sequence, ISAba10, inserted into ISAba1 adjacent to the blaOXA-23 gene and disrupting the outer membrane protein carO gene in Acinetobacter baumannii
Lee et al.,
Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 250 Seongsanno, Seodaemun-gu, Seoul 120-752, Korea; Korean Institute of Tuberculosis, 14 Woomyun-dong, Seocho-gu, Seoul 137-900, Korea
... higher level carbapenem resistance by conferring additional promoter sequences to the 85
blaOXA-23 gene. Analyses using an online tool (http://linux1.softberry.com) suggested the 86
presence of a putative promoter within the ISAba10 element (Fig. 1). 87 ...
Appl. Environ. Microbiol.
doi:10.1128/AEM.02417-09
Random mutagenesis of Clostridium cellulolyticum using a Tn1545 derivative
Jean-Charles Blouzard, Odile Valette, Chantal Tardif, and Pascale de Philip
Laboratoire de Chimie Bacterienne, IFR88-CNRS, Marseille, France; Universite d'Aix-Marseille, Marseille, France
...Promoter predictions (http://linux1.softberry.com/) at the 14 junctions of
pMIS1545 and the insertion sites revealed that putative -10/-35 promoters sites were 15 ...
Clinical Genetics
Volume 77, Issue 5, pages 453–463, May 2010 DOI: 10.1111/j.1399-0004.2009.01337.x
Novel exon nucleotide substitution at the splice junction causes a neonatal Marfan syndrome
Chao et al.,
1 Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, Douliou Branch, Yunlin, Taiwan
2 Institute of Basic Medical Sciences, National Cheng Kung University Medical College, Tainan, Taiwan
... The tools included Splice Site Prediction by Neural Network (NNSplice; http://www.fruitfly.org/
seq tools/splice.html) (9), a weight matrix-based prediction tool (Splm; http://linux1.softberry.com/
berry.phtml), NetGene2 (http://www.cbs.dtu.dk/services/ NetGene2/) (10), and ...
Mol Biotechnol.
2010 May;45(1):24-33
Characterization of a cryptic plasmid pD403 from Lactobacillus plantarum and construction of shuttle vectors based on its replicon
Sun Z, Kong J, Kong W
State Key Laboratory of Microbial Technology, Shandong University, Jinan, China.
... ncbi. nlm.nih.gov/Blast.cgi). Prediction of open reading frames, prokaryotic promoters,
and terminators was performed at http://opal.biology.gatech.edu/GeneMark/
gmhmm2_prok.cgi and http://www.softberry.com/berry.phtml. To ...
Electronic Journal of Biotechnology
DOI: 10.2225/vol13-issue5-fulltext-12
Isolation and characterization of the tissue and
development-specific potato snakin-1 promoter inducible
by temperature and wounding
Natalia I. Almasia 1 · Vanesa Narhirnak 1 · H. Esteban Hopp 1 · Cecilia Vazquez-Rovere 1
1 Instituto de Biotecnologia, Centro Nacional de Investigaciones Agropecuarias, Instituto Nacional de
Tecnologia Agropecuaria, Castelar, Los Reseros y Dr. N. Repetto, Hurlingham, Provincia de Buenos Aires, Argentina
... The amplified fragment was cloned in pCRII-TOPO® (TACloning®, Invitrogen (EUA),
sequenced and analyzed with the BioEdit Sequence Alignment Editor software,
Softberry, PlantCARE (Rombauts et al. 1999; Lescot et al. ...
The Plant Journal
61: 324–338. doi: 10.1111/j.1365-313X.2009.04057.x
Sucrose non-fermenting kinase 1 (SnRK1) coordinates metabolic and hormonal signals during pea cotyledon growth and differentiation
Radchuk et al.,
1 Institut fur Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany
2 Biology Department, Trent University, Peterborough, ON K9J 7B8, Canada
... Data bank searches (http://www.softberry.com) revealed a TTAGGGTTT motif described as an
inverted telo-box, associated with gene translation and the cell cycle (proliferating cell nuclear
antigen), a AATATTTTTATT motif found in pea ribulose-1,5-bisphosphate carboxylase ...
Plant Cell Rep.
2010 Mar;29(3):239-48
Isolation and functional characterization of two novel seed-specific promoters from sunflower (Helianthus annuus L.)
Zavallo D, Lopez Bilbao M, Hopp HE, Heinz R
Instituto de Biotecnologia, CNIA, Instituto Nacional de Tecnologia Agropecuaria-Castelar, Los Reseros y Nicolas Repeto, 1686 Hurlingham, Buenos Aires Province, Argentina
... Amplified fragments were cloned into pCR8/GW/TOPO (Invitrogen, USA), sequenced and analyzed
in silico with Vector NTI Advance 9 software (Invitrogen, USA). Pro- moter motif search was
conducted using Softberry server, PlantCARE database (Lescot et al. ...
PLoS
2010
Requirement of the galU Gene for Polysaccharide Production by and Pathogenicity and Growth In Planta of Xanthomonas citri subsp. citri
Yinping Guo, Uma Shankar Sagaram, Jeong-soon Kim, and Nian Wang
Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, IFAS, 700 Experiment Station Road, Lake Alfred, Florida 33850
... The intergenic distance between the galU gene and the downstream gene kefB is 174 bp.
The galU gene and the downstream kefB gene were predicted to belong to different operons
based on operon prediction using SOFTBERRY (Softberry, Inc.). ...
PLoS Biol
2010 8(8): e1000467. doi:10.1371/journal.pbio.1000467
Distinct Olfactory Signaling Mechanisms in the Malaria Vector Mosquito Anopheles
gambiae
Liu 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, Nashville, Tennessee, United States of America, 2 USDA, Agricultural Research Service, Henry A. Wallace Beltsville
Agricultural Research Center, Plant Sciences Institute, Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, United States of America
...Potential exon-intron gene
models were predicted based on homology to DmIRs or AgIRs, as
well as with the aid of a Hidden Markov Model-based gene structure predictor (www.Softberry.com)...
Journal of Bacteriology
October 2010, p. 5081-5092, Vol. 192, No. 19 doi:10.1128/JB.00653-10
The Delta Subunit of RNA Polymerase, RpoE, Is a Global Modulator of Streptococcus mutans Environmental Adaptation
Xiaoli Xue, Jurgen Tomasch, Helena Sztajer, and Irene Wagner-Dobler
esearch Group Microbial Communication, Division of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany
... S6 and S7 in the supplemental material) predicted by the SoftBerry web service (SoftBerry Inc.,
Mount Kisco, NY), while the third one had too short a sequence length (114 bp in total, but with
only 45 bp before the putative terminator) to find a putative promoter. ...
Journal of Bacteriology
May 2010, p. 2535-2545, Vol. 192, No. 10 doi:10.1128/JB.01689-09
A Genetic Determinant in Streptococcus gordonii Challis Encodes a Peptide with Activity Similar to That of Enterococcal Sex Pheromone cAM373, Which Facilitates Intergeneric DNA Transfer
Vickerman et al.,
Department of Periodontics and Endodontics and Department of Oral Biology, School of Dental Medicine, University at Buffalo, 223 Foster Hall, Buffalo, New York 14214,1 Cariology, Restorative Sciences and Endodontics, School of Dentistry,2
... oxidase signature (PS00079). The lspA gene is located between two overlapping
open reading frames with a single upstream promoter identified by both MacVector
and Softberry promoter prediction software. In silico analysis ...
Journal of Bacteriology
March 2010, p. 1184-1192, Vol. 192, No. 5 doi:10.1128/JB.01372-09
In Helicobacter pylori, LuxS Is a Key Enzyme in Cysteine Provision through a Reverse Transsulfuration Pathway
Doherty et al.,
Centre for Biomolecular Science, University of Nottingham, University Park, Nottingham NG7 2RD,1 Nottingham Digestive Diseases Centre NIHR Biomedical Research Unit, School of Clinical Sciences, University of Nottingham and Nottingham University Hospitals NHS Trust, Queen's Medical Centre, Nottingham NG7 2UH,2
... A putative 70 promoter lying upstream of cysK Hp was identified using promoter
prediction algorithms found at http://www.softberry.ru/berry.phtml and
http://www.fruitfly.org/seq_tools/promoter.html and is shown as an arrow. ...
Fungal Genetics and Biology
Volume 47, Issue 10, October 2010, Pages 818-827 doi:10.1016/j.fgb.2010.06.009
Specialized and shared functions of the histidine kinase- and HOG1 MAP kinase-mediated signaling pathways in Alternaria alternata, a filamentous fungal pathogen of citrus
Ching-Hsuan Lin a, b and Kuang-Ren Chung a, b
a Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS), University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
b Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL 32611, USA
... nlm.nih.gov/). Open 9 reading frame (ORF) and exon/intron positions were deduced
from comparisons of 10 genomic and cDNA sequences or predicted using the
gene-finding software at 11 http://www.softberry.com. A search ...
Research in Microbiology
Volume 161, Issue 2, March 2010, Pages 144-152 doi:10.1016/j.resmic.2009.12.002
The 285 kDa Bap/RTX hybrid cell surface protein (SO4317) of Shewanella oneidensis MR-1 is a key mediator of biofilm formation
Bjorn Vergauwen
a Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Ghent University, 9000 Ghent, Belgium
b Laboratory of Pharmaceutical Microbiology, Ghent University, 9000 Ghent, Belgium
.. A predicted promoter region (http://www.softberry.com) precedes the start site of ORF SO4317,
ORFs SO4318–SO4323 are separated from each other by no more than 27 base pairs, and an
intergenic region of 818 base pairs, containing a predicted transcription termination site ...
PLoS ONE
5(6): e11067. doi:10.1371/journal.pone.0011067
Genomic Features of the Human Dopamine Transporter Gene and Its Potential Epigenetic States: Implications for Phenotypic Diversity
Shumay E, Fowler JS, Volkow ND
1 Brookhaven National Laboratory, Medical Department, Upton, New York, United States of America, 2 National Institute on Drug Abuse, National Institutes of Health, Bethesda, Maryland, United States of America
... the typical sequence characteristics of a strong promoter. Here, de novo predicted
TSSs are only marginal (Promoter 2.0 Prediction server) or off-target (Softberry).
The software Eponine (Sanger) predicts multiple low-score ...
Chinese Science Bulletin
Volume 54, Number 18 / September, 2009 pp. 3249-3257
Characterization of a PDR type ABC transporter gene from wheat (Triticum aestivum L.)
Yi Shang et al.,
(1) State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing, 210095, China
(2) Institute of Crop Research and Nuclear Technique Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, 310021, China
... A positive TAC clone was identified using the primer pair SH49S and SH49A. The TAC
clone was sequenced us- ing a chromosome walking method and the gene was
predicted using Softberry software (http://www. soft- berry.com). ...
Mem. Inst. Oswaldo Cruz
vol.104 no.3 Rio de Janeiro May 2009 doi: 10.1590/S0074-02762009000300018
Phylogeny and evolution of the aspartyl protease family from clinically relevant Candida species
B Parra-Ortega; H Cruz-Torres; L Villa-Tanaca; C Herna'ndez-Rodri'guez
Departamento de Microbiologi'a, Escuela Nacional de Ciencias Biolo'gicas, Instituto Polite'cnico Nacional, Plan de Ayala y Prol. Carpio, Colonia Casco de Santo Toma's, CP 11340 Agencia de Correos 220, Me'xico, DF, Me'xico
... Prediction of motif sequences was performed with PROSITE (http://www.expasy.org) (Falquet
et al. 2002). PSORTII (http://www.psort.org/) and Softberry (http://www.softberry.com) were used
to predict subcellular localization; Softberry was also used to find exons. ...
Insect Biochemistry and Molecular Biology
Volume 39, Issue 8, August 2009, Pages 547-567
Comparative and functional genomics of lipases in holometabolous insects
Irene Horne, Victoria S. Haritos, John G. Oakeshott
CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601, Australia
encoded by href="genbank:XM_312606">XM_312606) to identify acid lipases; gene structures
were then predicted using Genscan (Burge and Karlin, 1997) or Softberry (http://www ...
Journal of Biomedicine and Biotechnology
Volume 2009 (2009), Article ID 398434, 10 pages
doi:10.1155/2009/398434
Adding to Yersinia enterocolitica Gene Pool Diversity: Two Cryptic Plasmids from a Biotype 1A Isolate
Lepka et al.,
Robert Koch Institute, Wernigerode Branch, Burgstrasse 37, 38855 Wernigerode, Germany
... resp.). 2.5. Sequence Analyses. Potential coding regions were determined by softberry
(http://www.softberry.com/) tools and confirmed applying Glimmer (http://www.ncbi.nlm.
nih.gov/genomes/MICROBES/glimmer_3.cgi). Comparison ...
Peptides
Volume 30, Issue 7, July 2009, Pages 1241-1248
FGLamide Allatostatin genes in Arthropoda: Introns early or late?
Francisco Marti'nez-Pe'rez a, b, William G. Benden ac, Belind a S.W. Chang a and Stephen S. Tobe a
aDepartment of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
bDepartment of Genetics and Molecular Biology, CINVESTAV, Mexico, D.F., Mexico
... from D. punctata and D. melanogaster. With the sequences obtained, the exon-intron
organization was established with Softberry programs (http://linux1.softberry.com/
berry.phtml). The conceptual translation and the sequence ...
Plant Molecular Biology
Volume 71, Numbers 1-2 / September, 2009, pp. 193-205
Cloning and characterization of two novel chloroplastic glycerol-3-phosphate dehydrogenases from Dunaliella viridis
Yunxia He et al.,
(1) Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, People’s Republic of China
(2) Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, People’s Republic of China
... al. 1997). Gene and protein predictions were carried out with the SoftBerry service
(http://www.softberry.com/berry.phtml). Possible chloroplast transit peptides were
predicted using ChloroP (http://www.cbs.dtu.dk/services/). Subcellular ...
Biochem. J.
(2009) 418, 443–451 (Printed in Great Britain) doi:10.1042/BJ20081478
Intracellular catalase/peroxidase from the phytopathogenic rice blast
fungus Magnaporthe grisea: expression analysis and biochemical
characterization of the recombinant protein
ZAMOCKY et al.,
*Metalloprotein Research Group, Division of Biochemistry, Department of Chemistry, University of Natural Resources and Applied Life Sciences, Muthgasse 18 A-1190 Vienna, Austria,
†Department of Chemistry, University of Modena and Reggio Emilia, Modena, Italy
... Promoter and subcellular targeting prediction Prediction of intron and native promoter location
within the geno- mic DNA of M. grisea strain 70-15 was performed in the SoftBerry suite
(http://www.softberry.com) using the ascomycete- specific parameters. ...
Applied and Environmental Microbiology
May 2009, p. 2869-2878, Vol. 75, No. 9 doi:10.1128/AEM.02326-08
Biosynthesis of Sibiromycin, a Potent Antitumor Antibiotic
Wei Li, Ankush Khullar, ShenChieh Chou, Ashley Sacramo, and Barbara Gerratana
Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
... ORF and sequence homology analyses were performed by using SoftBerry (Softberry, Inc.) and
GeneMark (exon.gatech.edu/GeneMark/) and by using BLAST programs (blast.ncbi.nlm.nih.gov/
blast.cgi), respectively. Production, isolation, and analysis of sibiromycin. ...
Molecular Genetics and Genomics
Volume 281, Number 1 / January, 2009 pp. 109-123
TRANSPARENTTESTA12 genes from Brassica napus and parental species: cloning, evolution, and differential involvement in yellow seed trait
You-Rong Chai et al.,
(1) Chongqing Rapeseed Engineering Research Center, Southwest University, Tiansheng Road 216#, Beibei, 400716 Chongqing, People’s Republic of China
(2) Chongqing Key Laboratory of Crop Quality Improvement, Southwest University, Tiansheng Road 216#, Beibei, 400716 Chongqing, People’s Republic of China
... Page 4. 112 Mol Genet Genomics (2009) 281:109-123 123 and websites such as NCBI
(http://www.ncbi.nlm.nih.gov), Expasy (http://www.expasy.org), and SoftBerry (http://www.
softberry.com). Southern hybridization for TT12 genes in B. napus and its two parental species ...
Plant Physiology Preview
Published on September 18, 2009; 10.1104/pp.109.145177
Metabolite sorting of a germplasm collection reveals the Hydroxylase3 locus as a new target for maize provitamin A biofortification
Ratnakar Vallabhaneni et al.,
Department of Biological Sciences, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, NY 10468; The Graduate School and University Center-CUNY, 365 Fifth Ave., New York, NY 10016-4309
... Gene models were drawn using Genscan (www.genscan.com), Softberry (www.softberry.
com) and Vector NTI Suite9.0 (Invitrogen, Carlsbad, CA). Transcription start sites were
estimated by EST and promoter analysis (www.softberry.com). ...
BMC Genomics
2009, 10:224doi:10.1186/1471-2164-10-224
Complete sequence determination of a novel reptile iridovirus isolated fromsoft-shelled turtle and evolutionary analysis of Iridoviridae
Youhua Huang et al.,
aState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 West Xingang Road, Guangzhou 510275, PR China
... programs at the NCBI website (http://www.ncbi.nlm.nih.gov). The whole genome sequence was
also submitted to http://www.softberry.com (Softberry Inc., Mount Kisco, NY, USA) for identification
of all putative ORFs. For more refined analyses, conserved motifs and domains and ...
Euphytica
Volume 167, Number 3 / June 2009, pp. 281-291
Promoter anchored amplified polymorphism based on random amplified polymorphic DNA (PAAP-RAPD) in cotton
Mingxiong Pang 1, R. G. Percy 2, Ed. Hughs 3 and Jinfa Zhang 1
(1) Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA
... information about the cloned PAAP-RAPD fragments, 220 plant promoter sequences were
downloaded from http://www.soft- berry.com and ... the cloned potential promoters we downloaded
the characterized dicot plant promoters from database at http://www.softberry.com/with a ...
Veterinary Immunology and Immunopathology
Volume 128, Issue 4, 15 April 2009, Pages 437-440
Complete sequencing of full-length canine ataxia telangiectasia mutated mRNA and characterization of its putative promoter
Fabio Gentilini, Maria Elena Turba, Monica Forni and Stefano Cinotti
aVeterinary Clinical Department, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064 - Ozzano Emilia, Bologna, Italy
... proscan/) (Prestridge, 1995) and "MOTIF" software (http://motif.genome.jp). The
putative PolyA signal sites were predicted using PolyA (http://www.softberry.com/).
Finally, the predictors PhD-SNP (http://gpcr.biocomp.unibo.it ...
International Journal of Hydrogen Energy
Volume 35, Issue 3, February 2010, Pages 1065-1073
Molecular characterization and homologous overexpression of [FeFe]-hydrogenase in Clostridium tyrobutyricum JM1
Ji Hye Jo, Che Ok Jeon, Seung Yoon Lee, Dae Sung Lee and Jong Moon Park
a Biosciences Center, National Renewable Energy Laboratory, 1617 Cole Blvd, Golden, CO 80401-3393, USA
... nucleotide identity. Transcription promoters and termination sequences of the hydA
gene were analyzed using web-based programs (http://www.softberry.com/;
http://www.fruitfly.org/seq.tools/promoters. html). The theoretical ...
Glycoconjugate Journal
Volume 26, Number 3 / April, 2009, pp. 313-324
Sialylation in protostomes: a perspective from Drosophila genetics and biochemistry
Kate Koles1, Elena Repnikova1, Galina Pavlova2, Leonid I. Korochkin2 and Vladislav M. Panin1
1) Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
... insect species: African malaria mosquito (Anopheles gambiae, XP_308850), yellow fever mosquito
(Aedes aegypti, XM_001649540), red flour beetle (Tribolium castaneum, XP_968750), and pea
aphid (Acyrthosiphon pisum, reconstructed using SoftBerry prediction (www.softberry.com) ...
Applied and Environmental Microbiology
November 2009, p. 6712-6720, Vol. 75, No. 21
Edwardsiella ictaluri Encodes an Acid-Activated Urease That Is Required for Intracellular Replication in Channel Catfish (Ictalurus punctatus) Macrophages
Natha J. Booth,1, Judith B. Beekman,1,2 and Ronald L. Thune 1,2*
Department of Veterinary Science, Louisiana State University Agricultural Center, Louisiana State University, Baton Rouge, Louisiana 70803,1 Department of Pathobiological Sciences, School of Veterinary Medicine, Skip Bertman Drive and River Road, Louisiana State University, Baton Rouge, Louisiana 708032
... The genetic structure of the urease operon was examined using the stem-loop and terminator
programs of the Wisconsin package (Genetics Computer Group, Madison, WI) and the bacterial
operon and gene-finding software program from SoftBerry, Inc. ...
Microb Cell Fact.
2009; 8: 48.
Surface display of heterologous proteins in Bacillus thuringiensis using a peptidoglycan hydrolase anchor
Xiaohu Shao,1 Mengtian Jiang,1 Ziniu Yu,1 Hao Cai,2 and Lin Li
1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
2College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
... kurstaki wild-type strain YBT-1520 comprises over 5600 ORFs (data not published). A
whole-genome analysis of the corresponding proteins in this strain was performed with the
online tool "softberry" [21], using the genome data of B. thuringiensis subsp. ...
The Plant Cell
21:131-145 (2009)
A Critical Role for the TIFY Motif in Repression of Jasmonate Signaling by a Stabilized Splice Variant of the JASMONATE ZIM-Domain Protein JAZ10 in Arabidopsis
Hoo Sun Chung a,b and Gregg A. Howe a,b
a Department of Energy–Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
b Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
... Gene prediction programs (www.softberry.com) suggest that JAZ10 orthologs in rice (Oryza sativa)
(gi:115458122) and poplar (Populus trichocarpa) (Joint Genome Institute gene model 548076)
are subject to alternative splicing events that alter the Jas domain. ...
MPMI
August 2009, Volume 22, Number 8
Pages 942-952
DOI: 10.1094/MPMI-22-8-0942
The YAP1 Homolog–Mediated Oxidative Stress Tolerance Is Crucial for Pathogenicity of the Necrotrophic Fungus Alternaria alternata in Citrus
Ching-Hsuan Lin, Siwy Ling Yang, and Kuang-Ren Chung
Citrus Research and Education Center, and Department of Plant Pathology, Institute of Food and Agricultural Sciences (IFAS), University of Florida, 700 Experiment Station Rd., Lake Alfred 33850, U.S.A.
... The pro- moter region was analyzed using regulatory sequence analysis tools. ORF
and exon or intron positions were predicted using Softberry gene-finding software
and verified by comparisons of genomic and cDNA sequences. ...
Journal of Plant Interactions
Volume 3, Issue 2 June 2008 , pages 75 - 93
Endophytes: exploiting biodiversity for the improvement of natural product-based drug discovery
Agata Staniek; Herman J. Woerdenbag; Oliver Kayser
Pharmaceutical Biology Department, University of Groningen, The Netherlands
... gramme (available from: http://www.softberry.com/ berry.phtml) aided by RACE (rapid
amplification of cDNA ends) and confirmed by reverse transcription- PCR ...
PLoS Genet
(2008) 4(1): e3. doi:10.1371/journal.pgen.0040003
Repetitive Element-Mediated Recombination as a Mechanism for New Gene Origination in Drosophila
Yang et al.,
Chinese Academy of Sciences (CAS)—Max Planck Junior Research Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
... copy-specific primers, and for those that resulted in no RACE product (possibly
due to low expression levels or long ends), we used the Softberry software [65 ...
Genetics.
2008 August; 179(4): 2239–2252. doi: 10.1534/genetics.108.089862
Quantitative Trait Loci (QTL) Analysis For Rice Grain Width and Fine Mapping of an Identified QTL Allele gw-5 in a Recombination Hotspot Region on Chromosome 5
Wan et al.,
National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China and †Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
... candidate genes in the 49.7-kb region (http://www.ncbi.nlm.nih.gov/BLAST;
http://www.softberry.com). Of these genes, one had unknown ...
Nucleic Acids Research
Volume 36(7)April 2008pp 2196-2207
Epigenetics of a tandem DNA repeat: chromatin DNaseI sensitivity and opposite methylation changes in cancers
Koji et al.,
Human Genetics Program and Department of Biochemistry and Tulane Cancer Center, Tulane Medical School, Tulane University, New Orleans, LA 70112, USA
... that p13E-11, which is only 0.1 kb from D4Z4 (Figure 1) and has no features of a
gene (http://exon.gatech.edu/GeneMark/ , http://www.softberry.com/berry.phtml ...
Cell Research
18, 1199 - 1209 (01 Dec 2008), doi: 10.1038/cr.2008.307
Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight
Weng et al.,
... (D) Compared with IR24, 1.2-kb genomic DNA is deleted in Asominori. (E) Three ORFs
are predicted in the candidate region harboring GW5 (http://softberry.com). ...
PROTEOMICS
2008, Volume 8 Issue 20, Pages 4273 - 4286
Physiology of Streptococcus thermophilus during the late stage of milk fermentation with special regard to sulfur amino-acid metabolism
Herve-Jimenez et al.,
INRA,UR477 Biochimie Bacterienne, Jouy-en-Josas, France
... a) L/E ratio: ratio between the relative mRNA levels at 5h30 and 2h30. b) Determined
with ProFinder software (http://www.softberry.com/all.htm). ...
BMC Microbiology
2008, 8:227 doi:10.1186/1471-2180-8-227
Genomic analysis of bacteriophage epsilon34 of Salmonella enterica serovar
Anatum (15+)
Robert Villafane, Milka Zayas, Eddie B. Gilcrease, Andrew M. Kropinski, and Sherwood R. Casjens
Ponce School of Medicine,
Departments of Biochemistry and Microbiology,
Ponce, Puerto Rico 00732
The Betawrap
Published in Crop Sci
48:2314-2320 (2008)
Cloning and Characterization of a CAP Gene Expressed in Gossypium arboreum Fuzzless Mutant
Sheng Wang, Guo-Hong Zhao, Yin-Hua Jia and Xiong-Ming Du
Cotton Germplasm Division, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Huanghe Dadao, Kaifaqu, Anyang, Henan 455000, China
... Blast.cgi). Softberry server was used to determine the exon/intron boundaries
(http://www.softberry.com/berry.phtml). The conceptual ...
J Microbiol Methods.
2008 May;73(2):133-41. Epub 2008 Feb 11
An integrative expression vector for strain improvement and environmental applications of the nitrogen fixing cyanobacterium, Anabaena sp. strain PCC7120
Chaurasia AK, Parasnis A, Apte SK
Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India.
... 164 base pair region upstream of psbA1) showed 50% homology with the ? 10 and ?
35 consensus sequences of E. coli promoters (www.softberry.com/promoscan). ...
The Journal of Immunology
2008, 181: 7106-7114.
Histoplasma capsulatum Cyclophilin A Mediates Attachment to Dendritic Cell VLA-5
Francisco J. Gomez, Robyn Pilcher-Roberts, Arash Alborzi and Simon L. Newman
Department of Internal Medicine, Division of Infectious Diseases, University of Cincinnati College of Medicine, and {dagger} Veterans Administration Medical Center, Cincinnati, OH 45267
... The sequence was analyzed with the SoftBerry GeneFinder on-line server
(http://www.softberry.com/berry.phtml) that correctly identified the Hc CypA coding ...
Biochemical Journal Immediate Publication.
Published on 10 Nov 2008 as manuscript BJ20081478
Intracellular catalase-peroxidase
from the phytopathogenic fungus Magnaporthe grisea:
expression analysis and biochemical characterisation
of the recombinant protein
Zamocky et al.,
Metalloprotein Research Group, Division of Biochemistry, Department of Chemistry,
University of Natural Resources and Applied Life Sciences, Muthgasse 18 A-1190 Vienna,
Austria
... Prediction of intron and native promoter location within the genomic DNA of Magnaporthe
grisea strain 70-15 was performed in SoftBerry suite (http://www ...
Bioscience, Biotechnology, and Biochemistry
Vol. 72 (2008) , No. 6 pp.1571-1579
Molecular Cloning, Characterization, and Differential Expression of a Farnesyl-Diphosphate Synthase Gene from the Basidiomycetous Fungus Ganoderma lucidum
Yi-Xin DING et al.,
College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture
... The phylogenetic tree was gener- ated by MEGA. 18) The promoter sequences were analyzed
online at the http://www.softberry.com/ berry.phtml website. Results ...
Applied and Environmental Microbiology
July 2008, p. 4359-4365, Vol. 74, No. 14 doi:10.1128/AEM.02499-07
Novel Bacterial Surface Display Systems Based on Outer Membrane Anchoring Elements from the Marine Bacterium Vibrio anguillarum
Zhao Yang, Qin Liu,* Qiyao Wang, and Yuanxing Zhang*
State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
... of the above membrane-related proteins were analyzed with ExPASy Proteomics tools
(TMHMM Server v.2.0 [http://kr.expasy.org/tools/]) and SoftBerry (data not ...
MPMI
April 2008, Volume 21, Number 4, Pages 469-479 DOI: 10.1094/MPMI-21-4-0469
Genetic Dissection Defines the Roles of Elsinochrome Phytotoxin for Fungal Pathogenesis and Conidiation of the Citrus Pathogen Elsinoe fawcettii
Hui-Ling Liao and Kuang-Ren Chung
Citrus Research and Education Center, and Department of Plant Pathology, Institute of Food and Agricultural Sciences (IFAS), University of Florida, 700 Experiment Station Rd., Lake Alfred 33850, U.S.A.
... ORF and exon/intron positions were predicted using the Softberry gene-finding software
and confirmed by comparisons of genomic and cDNA sequences. ...
Microbiology
154 (2008), 3556-3566; DOI 10.1099/mic.0.2008/019414-0
Determination of a transcriptional regulator-like gene involved in biosynthesis of elsinochrome phytotoxin by the citrus scab fungus, Elsinoe fawcettii
Kuang-Ren Chung and Hui-Ling Liao
Citrus Research and Education Center, and Department of Plant Pathology, Institute of Food and Agricultural Sciences (IFAS), University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
... Prediction of ORFs and exon/intron junctions was first performed using the
gene-finding software at http://www.softberry.com and further confirmed by comparing ...
BMC Genomics
2008; 9: 149. Published online 2008 March 31. doi: 10.1186/1471-2164-9-149.
Losing helena: The extinction of a drosophila line-like element
Rita Rebollo, Emmanuelle Lerat, Liliana Lopez Kleine, Christian Biemont, and Cristina Vieira
1Universite de Lyon; Universite Lyon 1; CNRS; UMR 5558, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne F-69622, France
2UR477 de Biochimie Bacterienne, UR341 de Mathematiques et informatiques Applique'es, INRA. 78352 Jouy en Josas, France
... Splice sites and transcription binding sites were predicted by the Softberry tools
[40] and Genomatix [41]; PEPcoil ([42] allowed us to find the coiled coil ...
Blood Coagulation & Fibrinolysis.
19(3):240-242, April 2008
Four novel FXI gene mutations in three factor XI- deficient patients
de Raucourt, Emmanuelle a; de Mazancourt, Philippe b,c; Quelin, Florence b,c
... to the acceptor site for exon 7, but an exon prediction software did not show an
effect on the probability of splicing (website: http://www.softberry.com/cgi ...
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-Rehbrucke, Department of Nutritional Toxicology, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
... then used the Baylor College of Medicine (BCM) Search Launcher http://searchlauncher.
bcm.tmc.edu/ (many modules are now hosted by http://www.softberry.com) to ...
Infection and Immunity
June 2008, p. 2411-2419, Vol. 76, No. 6
Identification of a Novel Prophage-Like Gene Cluster Actively Expressed in Both Virulent and Avirulent Strains of Leptospira interrogans Serovar Lai
Jin-Hong Qin et al.,
Department of Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China,1 Laboratory of Molecular Microbiology, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
... uk/). Transcription operons and the corresponding promoters were predicted
using Softberry software (Softberry, Mount Kisco, NY). ...
...The putative
promoter or regulatory regions of transcripts I, II, and
III, all proximal to gene LA0195 but with different transcription
directions, were identified by using the Softberry prokaryotic
promoter prediction tools....
Molecular Immunology
Volume 45, Issue 12, July 2008, Pages 3470-3476
IgD in the reptile leopard gecko
Francisco Gambon-Deza and Christian Sanchez Espinel
Unidad de Inmunologia, Hospital do Meixoeiro, Carretera de Madrid s/n, Vigo 36210, Pontevedra, Spain
... Sequence characteristics were analysed in the Softberry Web to deduce the exons
and introns, and to verify the presence of other interesting characteristics ...
Endocrinology
2008 Vol. 149, No. 9 4256-4266
Seladin-1 Is a Fundamental Mediator of the Neuroprotective Effects of Estrogen in Human Neuroblast Long-Term Cell Cultures
Paola Luciani et al.,
Endocrine Unit, Department of Clinical Physiopathology, Center for Research, Transfer and High Education on Chronic, Inflammatory, Degenerative and Neoplastic Disorders for the Development of Novel Therapies (P.L., C.D., F.R., S.B., I.C., F.D., M.M., G.D., M.S., A.P.), Department of Anatomy, Histology, and Forensic Medicine (G.B.V.), University of Florence, 50139 Florence, Italy
... A 6-kb region upstream seladin-1 open reading frame was analyzed using eukaryotic
promoter identification programs (http://www.softberry.com/berry.phtml? ...
Biochimie
Volume 90, Issue 6, June 2008, Pages 878-887
Fish specific duplication of Dmrt2: Characterization of zebrafish Dmrt2b
Xiang Zhou et al.,
Department of Genetics and Center for Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
... www.ensembl.org/Danio_rerio/), and the exons of Dmrt2b were predicted by CBS PREDICTION
SERVERS (http://www.cbs.dtu.dk/services/) and SOFTBERRY (http://www ...
PNAS
February 27, 2007 | vol. 104 | no. 9 | 3336-3341
A common variant in combination with a nonsense mutation in a member of the thioredoxin family causes primary ciliary dyskinesia
Benedicte Duriez et al.,
Institut National de la Sante et de la Recherche Medicale,
Unite 654, F-94000 Creteil, France; Faculte de Me'decine,
Universite Paris 12, IFR10, F-94000 Creteil, France
... in Man, www.ncbi.nlm.nih.gov/Omim (for PCD and Kartagener syndrome); Ensembl,
www.ensembl.org; NCBI, www.ncbi.nlm.nih.gov; and Softberry, www.softberry.com. ...
Journal of Bacteriology,
October 2007, p. 6928-6935, Vol. 189, No. 19
Negative Regulation of the EcoRI Restriction Enzyme Gene Is Associated with Intragenic Reverse Promoters
Yaoping Liu, and Ichizo Kobayashi
Department of Medical Genome Sciences, Graduate School of Frontier Science, University of Tokyo, Tokyo, Japan,1 Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
... rebase.html). In silico promoter prediction was carried out with the tools
available at http://www.softberry.com/all.htm. The RNA ...
Applied and Environmental Microbiology,
November 2007, p. 7367-7372, Vol. 73, No. 22
Regulation of a Novel Acidithiobacillus caldus Gene Cluster Involved in Metabolism of Reduced Inorganic Sulfur Compounds
Olena I. Rzhepishevska et al.,
Molecular Biology, Umea* University, SE-901 87 Umea*, Sweden,
... Promoter prediction was performed using programs available at www.fruitfly.org/
seq_tools/promoter.html and www.softberry.com and a combined Hidden Markov Model ...
Journal of Plant Physiology
Volume 164, Issue 3, 7 March 2007, Pages 350-363
Cloning and molecular characterization of a functional flavonoid 3'-hydroxylase gene from Brassica napus
Ben-Bo Xu et al.,
Chongqing Rapeseed Technology Research Center, Chongqing Key Laboratory of Crop Quality Improvement, Beibei, Chongqing 400716, People's Republic of China
... gov/). Protein structure predictions were carried out on websites
(http://www.expasy.org and http://www.softberry.com/berry.phtml). ...
Biochemical and Biophysical Research Communications
Volume 358, Issue 2, 29 June 2007, Pages 590-595
Activation-induced changes in alternate splice acceptor site usage
T. Prescott Atkinson and Yuling Dai
Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA
... A list of over 12,000 publicly available EST-verified human splice acceptor sites
(www.softberry.com) was examined for the occurrence of the AGCAG motif, and ...
Journal of Bacteriology,
March 2007, p. 1774-1782, Vol. 189, No. 5
The fox Operon from Rhodobacter Strain SW2 Promotes Phototrophic Fe(II) Oxidation in Rhodobacter capsulatus SB1003
Laura R. Croal, Yongqin Jiao, and Dianne K. Newman
Division of Biology, Division of Geological and Planetary Sciences, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125
... Predicted operons, promoters, and terminators were identified with the
tools at Softberry (http://www.softberry.com/berry.phtml). ...
Crop Sci
47:2437-2444 (2007)
Identification, Characterization and Expression of Drought Related alpha-Crystalline Heat Shock Protein Gene (GHSP26) from Desi Cotton
Asma Maqbool et al.,
Center of Excellence in Molecular Biology, University of the Punjab, 87-Canal Bank Road, Thokar Niaz Baig Lahore (53700) Pakistan
... 2007). To find out the exon/intron boundaries, untranslated regions (UTRs), and
poly-A tail, softberry server was used (http://www.softberry.com/berry.phtml). ...
Plant Molecular Biology
Volume 65, Number 4 / November 2007 p. 453-466
T-DNA tagged knockout mutation of rice OsGSK1 , an orthologue of Arabidopsis BIN2 ,
with enhanced tolerance to various abiotic stresses
Serry Koh et al.,
Department of Life Science, Sogang University, Seoul, 121-742, Korea
... 2002), and were annotated with the Softberry program (http://www. softberry.com/
berry.phtml), and BLASTP (http://www. ncbi.nlm.nih.gov/BLAST). ...
Molecular Immunology
doi:10.1016/j.molimm.2007.09.015
Global identification and comparative analysis of SOCS genes in fish: Insights into the molecular evolution of SOCS family
Hong-Jian Jin, Jian-Zhong Shao, Li-Xin Xiang, Hao Wanga and Li-Li Sun
College of Life Sciences, Zhejiang University, Hangzhou 310058, China
... search coding exons or open reading frames (ORF) by the GENSCAN program
(http://genes.mit.edu/GENSCAN.html) or GENE FINDING programs at the Softberry web ...
Archives of Virology
Volume 152, Number 8 / August 2007 p. 1457-1465
Characterization of complete genome sequence of the spring viremia of carp
virus isolated from common carp (Cyprinus carpio) in China
Y. Teng et al.,
State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
... the genomic map. Putative ORFs were predicted by submitting to http:==
www.softberry.com (Softberry Inc., Mount Kisco, NY). In all ...
Molecular and Biochemical Parasitology
Volume 154, Issue 1, July 2007, Pages 52-61
Are Caenorhabditis elegans receptors useful targets for drug discovery:
Pharmacological comparison of tyramine receptors with high identity
from C. elegans (TYRA-2) and Brugia malayi (Bm4)
Katherine A. Smith, Elizabeth B. Rex and Richard W. Komunieck
Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606-3390, USA
... were performed with TYRA-2. Contigs with high matches to C. elegans proteins
were run through a modified gene prediction program, Softberry (http://sun1 ...
Biochemical and Biophysical Research Communications
Volume 358, Issue 4, 13 July 2007, Pages 1148-1153
Characterization of two temperature-inducible promoters newly isolated from B. subtilis
Wang Li et al.,
College of Animal Sciences, Northwest A&F University, Yangling 712100,
People’s Republic of China
... The sequence analysis was performed online with NCBI blast 2.0 (www.ebi.ac.uk);
promoter region was predicted by softberry software (www.softberry.com). ...
Biochemical and Biophysical Research Communications
Volume 354, Issue 1, 2 March 2007, Pages 90-95
Assay and characterization of a strong promoter element from B. subtilis
Ai-Ling Zhang et al.,
College of Animal Sciences, Northwest A&F University, Yangling 712100,
People’s Republic of China
... The sequence analysis was performed online with NCBI blast (http://www.ncbi.nih.
gov), and promoters were predicted online by using of softberry (http://www ...
Crop Sci
47:14-26 (2007)
The FAD2 Gene Family of Soybean:
Insights into the Structural and Functional Divergence of a Paleopolyploid Genome
Jessica A. Schlueter et al.,
USDA-ARS-CICGR, Ames, IA 50011
... based parameters (www.softberry.com; verified 13 Dec. 2006), and GeneMark.hmm with
A. thaliana based parameters (Lukashin and Borodovsky, 1998) were run. ...
J Gen Virol
88 (2007), 450-457; DOI 10.1099/vir.0.82396-0
Genome organization of the Chelonus inanitus
polydnavirus: excision sites, spacers and abundance of proviral and excised segments
Marc Annaheim and Beatrice Lanzrein
Institute of Cell Biology, Baltzerstrasse 4, CH-3012 Bern, Switzerland
... Gene prediction with Softberry software suggested the presence of a gene with
a deduced product of 57 amino acids and two exons on the spacer. ...
Molecular Biology and Evolution
2007 24(2):539-550; doi:10.1093/molbev/msl183
Mechanisms and Rates of Birth and Death of Dispersed Duplicated Genes during the Evolution of a Multigene Family in Diploid and Tetraploid Wheats
Eduard D. Akhunov, Alina R. Akhunova and Jan Dvorak
Department of Plant Sciences, University of California, Davis
... No known promoter or enhancer elements were found with the promoter
prediction software
(www.softberry.com/berry.phtml) within a 1,297-bp sequenced region ...
Journal of Bacteriology
March 2007, p. 1774-1782, Vol. 189, No. 5
The fox Operon from Rhodobacter Strain SW2 Promotes
Phototrophic Fe(II) Oxidation in Rhodobacter capsulatus SB1003
Laura R. Croal, Yongqin Jiao, and Dianne K. Newman
Division of Biology, Division of Geological and Planetary Sciences, Howard Hughes Medical Institute,
California Institute of Technology, Pasadena, California 91125
... Predicted operons, promoters, and terminators were identified with the
tools at Softberry (http://www.softberry.com/berry.phtml). ...
PLoS Comput Biol
2006 2(3): e18 doi:10.1371/journal.pcbi.0020018
A Third Approach to Gene Prediction Suggests Thousands of Additional Human Transcribed Regions
Glusman G, Qin S, El-Gewely MR, Siegel AF, Roach JC, et al.
1 Institute for Systems Biology, Seattle, Washington, United States of America, 2 Institute of Medical Biology, University of Tromso, Tromso, Norway, 3 Departments of Management Science, Finance and Statistics, University of Washington, Seattle, Washington, United States of America
...We include here the genomewide annotation of known genes (KG), Ensembl genes (ENS), Twinscan (TW),
GenScan (GS), Softberry genes (SB)..
Infection and Immunity,
January 2006, p. 410-424, Vol. 74, No. 1
DNA Adenine Methyltransferase Influences the Virulence of
Aeromonas hydrophila
Tatiana E. Erova et al.,
Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555-1070
... Putative -10 (GGGTAGAAT) and -35 (TAGCCA) elements of the promoter were also identified
in this region using a software program found at www.softberry.com. ...
Molecular Microbiology
Volume 59 Issue 2 Page 707-721, January 2006
Evidence for siderophore-dependent iron acquisition in group B streptococcus
Anne Clancy et al.,
1Division of Infectious Diseases, Immunology, and Rheumatology, Department of Pediatrics, Children's Hospital and Regional Medical Center/University of Washington, 307 Westlake Avenue N, Seattle WA 98109, USA.
2
Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada N6A 5C1.
... The promoter prediction programs utilized were http:/ / www.fruitfly.org/ seq_tools/
promoter.html and http:/ / www.softberry.com/ berry.phtml?topic=promoter . ...
Infection and Immunity,
October 2006, p. 5763-5772, Vol. 74, No. 10
Mutations within the Catalytic Motif of DNA Adenine
Methyltransferase (Dam) of Aeromonas hydrophila Cause the
Virulence of the Dam-Overproducing Strain To Revert to
That of the Wild-Type Phenotype
Tatiana E. Erova et al.,
Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, Texas 77555-1070
... be methylated by Dam, resulting in increased Act production, were detected within
the putative promoter region by using a software program from Softberry, Inc. ...
JBC Papers in Press.
Published on May 15, 2006 as Manuscript M601307200
Importance of CREB in Regulation of Expression of the Murine Cyclic Nucleotide
Phosphodiesterase 3B (PDE3B) Gene in Differentiating 3T3-L1 Preadipocytes
Hanguan Liu et al.,
Pulmonary/Critical Care Medicine Branch, National Heart, Lung, and Blood Institute, National
Institutes of Health, Bethesda, MD 20892 and +Section for Molecular Signaling, Department of Cell
and Molecular Biology, University of Lund, S-22100, Lund, Sweden
Consistent with our experimental results, two promoter regions
(beginning at position -4061 and another, at-364)
were predicted when 5105 bp of the 5’-flanking sequence of the murine
PDE3B gene was queried at http://www.softberry.com/all.htm.
Molecular Biology and Evolution
2006 23(7):1386-1396; doi:10.1093/molbev/msl004
Molecular Characterization of a Diagnostic DNA Marker for Domesticated Tetraploid Wheat Provides Evidence for Gene Flow from Wild Tetraploid Wheat to Hexaploid Wheat
Jan Dvorak, Eduard D. Akhunov, Alina R. Akhunov, Karin R. Deal and Ming-Cheng Luo
Department of Plant Sciences, University of California, Davis
A putative transcription start was identified 166 bp upstream of the translation start by
searching promoter a database at http://www.softberry.com/berry.phtml.
Genetics,
Vol. 172, 1251-1261, February 2006
The Maize aberrant pollen transmission 1 Gene Is a SABRE/KIP Homolog
Required for Pollen Tube Growth
Zhennan Xu*, and Hugo K. Dooner*
* Waksman Institute, Rutgers University, Piscataway, New Jersey 08855 and
Department of Plant Biology, Rutgers University, New Brunswick, New Jersey 08901
...The exon–intron
junctions of the rice SAK genes were determined
with the Softberry sequence analysis program (http://
www.softberry.com/berry.phtml), aided by the maize
apt1 full-length cDNA sequence....
Science
28 April 2006:
Vol. 312. no. 5773, pp. 583 - 588
Global Control of Dimorphism and Virulence in Fungi
Julie C. Nemecek,1 Marcel Wuthrich,2 Bruce S. Klein
Department of Medical Microbiology and Immunology, University of Wisconsin Medical School, University of Wisconsin Hospital and Clinics, Madison, WI 53792, USA.
... ORFA encodes a protein of 1274 residues (on the basis of transcript size) and
predicted by gene-finding software (Softberry, Mount Kisco, NY). ...
Applied and Environmental Microbiology
February 2006, p. 1086-1095, Vol. 72, No. 2
The Naphthalene Catabolic (nag) Genes of Polaromonas naphthalenivorans CJ2:
Evolutionary Implications for Two Gene Clusters and Novel Regulatory Control
Che Ok Jeon,1,2 Minjeong Park,2 Hyun-Su Ro,2,3 Woojun Park,4 and Eugene L. Madsen1
Department of Microbiology, Cornell University, Ithaca, New York 14853-8101,
1 Division of Environmental Biotechnology, EBNCRC & PMBBRC, Gyeongsang National University, 900 Gazwa-dong, JinJu, GyeongNam 660-701, Korea,
... 1). Transcription promoters and termination sequences of the nag gene clusters were
analyzed by using web-based programs (http://www.softberry.com/; http://www ...
Blood Coagulation & Fibrinolysis.
17(1):69-73, January 2006.
Identification of five novel mutations in the factor XI gene (F11) of patients with factor XI deficiency
Quelin, Florence et al.,
... NetGene2/ ; http://www.fruitfly.org/cgi-bin/seq_tools/splice.pl ; http://125.itba.
mi.cnr.it/?webgene/wwwspliceview.html ; http://www.softberry.com/cgi-bin ...
Acta Biochimica et Biophysica Sinica,
Volume 38, Number 7, July 2006 , pp. 492-499(8)
OsFY, a Homolog of AtFY, Encodes a Protein that
Can Interact with OsFCA-g in Rice (Oryza sativa L.)
LU, Qi; XU, Zheng-Kai; SONG, Ren-Tao
Shanghai Key Laboratory of Bio-energy Crop, School of Life Sciences, Shanghai University, Shanghai 200444, China
... AP003735). We predicted OsFY mRNA using HMM-based gene structure prediction with
the monocot setting at http:/ /www.softberry.com/berry.phtml. ...
Archives of Microbiology
Volume 186, Number 6 / December, 2006 513-517
The ntp operon encoding the Na+ V-ATPase of
the thermophile Caloramator fervidus
Trees Ubbink-Kok1, Jeroen Nijland1, Dirk-Jan Slotboom2 and Juke S. Lolkema1
(1) Molecular Microbiology, Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN, Haren, Groningen, The Netherlands
(2) Membrane Enzymology, Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
... related organ- isms. Putative promoters and terminators were identi- Wed
at http://www.softberry.com/berry.phtml. The sequence was ...
Molecular Biology and Evolution
2006 23(3):550-558
Molecular Evolution of the Ankyrin Gene Family
Xinjiang Cai, and Yanhong Zhang
Howard Hughes Medical Institute and Departments of Cell Biology, Biochemistry, and Neuroscience, Duke University Medical Center and Department of Medicine, Duke University Medical Center
... open reading frames using the GENSCAN program (Burge and Karlin 1997 Go)
(http://genes.mit.edu/GENSCAN.html) or GENE FINDING programs at the Softberry Web ...
DNA Sequence
Volume 17, Issue 1 February 2006 , pages 31 - 40
Alternative splicing and expression analysis of
OsFCA (FCA in Oryza sativa L.), a gene homologous to FCA in Arabidopsis
Xiling Du; Xiaoyin Qian; Dong Wang; Jinshui Yang
Institute of Genetics, School of Life Sciences, Fudan University. Shanghai. China
... The obtained genomic sequence was sent to Softberry (www.softberry.com) to predict
the sequence of full length cDNA of OsFCA. ... Softberry (www.softberry.com). ...
Applied and Environmental Microbiology
February 2006, p. 1496-1506, Vol. 72, No. 2
Paenibacillus sp. Strain JDR-2 and XynA1: a Novel System for Methylglucuronoxylan Utilization
Franz J. StJohn, John D. Rice, and James F. Preston*
Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
... Analysis of sequences for regulatory elements was conducted using the online tools
available through Softberry (http://www.softberry.com/berry.phtml). ...
Microbiology
151 (2005), 1671-1682; DOI 10.1099/mic.0.27848-0
mrpA, a gene with roles in resistance to Na+ and adaptation to alkaline pH in the cyanobacterium Anabaena sp. PCC7120
A. Blanco-Rivero1,, F. Leganes1, E. Fernandez-Valiente1, P. Calle2 and F. Fernandez-Pinas1
1 Departamento de Biologia, Facultad de Ciencias, Universidad Autonoma de Madrid, Madrid 28049, Spain
2 Departamento de Quimica Fisica Aplicada, Universidad Autonoma de Madrid, Madrid 28049, Spain
... A promoter-like sequence (-35 region and -10 region; http://www.softberry.com/
berry.phtml) was found in the upstream region (data not shown). ...
Journal of Bacteriology
December 2005, p. 8247-8255, Vol. 187, No. 24 doi:10.1128/JB.187.24.8247-8255.2005
Distribution and Expression of the ZmpA Metalloprotease in the Burkholderia cepacia Complex
S. Gingues, C. Kooi, M. B. Visser, B. Subsin, and P. A. Sokol
Department of Microbiology & Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
... promoter sequences of J2315 and Pc715j zmpA were compared and found to be identical
in both the -35 (TTGTAA) and -10 (TTCTAGCAT) regions (www.softberry.com ...
Current Microbiology
Volume 50, Number 3 / March, 2005 pp. 129-132
Characterization of a 4 kb Variant of the nifD Element in Anabaena sp. Strain ATCC 33047
Brian J. Henson1, Linda E. Watson1 and Susan R. Barnum1
(1) Department of Botany, Miami University, Oxford, OH 45056, USA
... ORF searches were performed with the NCBI ORF finder (www.ncbi.nlm.nih.gov), Gene
Finder (www.softberry.com), and Gene Mark (http://opa1.biology.gatech.edu ...
Microbiology
151 (2005), 1381-1393; DOI 10.1099/mic.0.27718-0
Enterococcus faecalis divIVA: an essential gene involved in cell division, cell growth and chromosome segregation
Sandra Ramirez-Arcos1,2,, Mingmin Liao1, Susan Marthaler1, Marc Rigden1 and Jo-Anne R. Dillon1,2,
1 Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada K1H 8M5
2 Centre for Research in Biopharmaceuticals and Biotechnology, University of Ottawa, Ottawa, ON, Canada K1H 8M5
... and the presence of putative promoters and transcriptional terminators in the E.
faecalis dcw gene cluster was completed using http://sun1.softberry.com/berry ...
Journal of Experimental Botany
2005 56(414):1177-1188; doi:10.1093/jxb/eri110
Molecular characterization of DNA sequences from the Primula vulgaris S-locus
Manfield et al.,
Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
... Prediction of putative genes structures was undertaken using gene prediction software
using the default parameters (www.softberry.com/berry.phtml). Results. ...
Antimicrobial Agents and Chemotherapy
April 2005, p. 1432-1440, Vol. 49, No. 4 doi:10.1128/AAC.49.4.1432-1440.20
Acquisition of Resistance to Carbapenems in Multidrug-Resistant Clinical Strains of Acinetobacter baumannii: Natural Insertional Inactivation of a Gene Encoding a Member of a Novel Family of ?-Barrel Outer Membrane Proteins
Maria A. Mussi, Adriana S. Limansky, and Alejandro M. Viale
Instituto de Biologia Molecular y Celular de Rosario (IBR, CONICET) and Departamento de Microbiologia, Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, Rosario, Argentina
... Predictions of consensus bacterial promoter sequences were conducted at
http://www.softberry.com. Nucleotide sequence accession numbers. ...
Nucleic Acids Research
2005 33(5):1739; doi:10.1093/nar/gki320
Human pol II promoter prediction: time series descriptors and machine learning
Rajeev Gangal and Pankaj Sharma
SciNova Technologies Pvt. Ltd 528/43 Vishwashobha, Adjacent to Modi Ganpati, Narayan Peth, Pune 411030, Maharashtra, India
... for promoter prediction, eg Neural Network Promoter Prediction (http://www.fruitfly.
org/seq_tools/promoter.html), SoftBerry (http://www.softberry.com/berry ...
Plant Molecular Biology
Volume 58, Number 3 / June, 2005 pp.421-433
OsPPR1, a pentatricopeptide repeat protein of rice is essential for the chloroplast biogenesis
Kodiveri M. Gothandam1, Eun-Sook Kim1, Hongjoo Cho1 and Yong-Yoon Chung1
(1) School of Life Sciences and Biotechnology, Korea University, Sungbuk-ku, 136-701, Seoul, Anam-Dong, Korea
... nucleotide and amino acid sequences were analyzed by the Basic Local Alignment Search
Tool (BLAST) and the Softberry prog- rame (http://www.softberry.com/). ...
Mol Cells.
2005 Apr 30;19(2):212-8.
Characterization of an abiotic stress-inducible dehydrin gene, OsDhn1, in rice (Oryza sativa L.)
Lee SC et al.,
Department of Life Science, Sogang University, Seoul 121-742, Korea
... genomic sequences were retrieved (with E-values < 3.8) all of which contained putative
dehydrin genes as predicted by the annotation tool, Softberry (http://www ...
Microbiol Res.
2005;160(3):233-42.
Salt stress induction of glutamyl endopeptidase biosynthesis in Bacillus intermedius
Gabdrakhmanova et al.,
Department of Microbiology, Kazan State University, Kazan, Russia
... was inspected for the occurrence of the characteristic -35 and -10 boxes of
SigA-type promoters (Helmann, 1995) by using the Softberry Prediction of ...
Biochim Biophys Acta.
2005 Jan 3;1739(2-3):140-9
Potential structure/function relationships of predicted secondary structural elements of tau
Gamblin TC.
Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave. Lawrence, KS 66045, USA
... sequence [17]. This analysis was originally performed on-line, and is now
available at http://www.softberry.com/berry.phtml. The ...
Microbiology
150 (2004), 518-520; DOI 10.1099/mic.0.26871-0
IVET experiments in Pseudomonas fluorescens reveal cryptic promoters at loci associated with recognizable overlapping genes
Mark W. Silby1, Paul B. Rainey2,3 and Stuart B. Levy1,4
1 Center for Adaptation Genetics and Drug Resistance, Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
...Using SoftBerry software (http://www.softberry.com/berry.phtml), -35 and -10 boxes and a transcriptional start site were predicted 84, 60 and 44 bp upstream of the iiv5 ORF, respectively...
alzheimer’s disease brain
Journal Journal of Molecular Neuroscience
Volume 24, Number 2 / June, 2004 pp.269-275
The splicing regulatory protein p18SRP is down-regulated in alzheimer’s disease brain
Heese et al.,
(1) BF Research Institute, c/o National Cardiovascular Center, 565-0873 Suita, Osaka, Japan
(2) Choju Medical Institute, Fukushimura Hospital, Noyori, 441-8124 Toyohashi, Aichi, Japan
... Protein sequence analysis was per- formed with Prosite, Profile, Blocks, ProDom,
Prints, Pfam, PsortII, Softberry, AACompIdent, Inter- ProScan, SMART,and ELM ...
Plant Science
Volume 166, Issue 1, January 2004, Pages 69-79
Trapping and characterization of cold-responsive genes from T-DNA tagging lines in rice
Lee et al.,
a Department of Life Science, Sogang University, Seoul 121-742, South Korea
b Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, South Korea
... database, and were annotated using the Rice Genome Automated Annotation System
(RiceGAAS; http://www.ricegaas.dna.affrc.go.jp), the Softberry program (http ...
Plant Molecular Biology
Volume 54, Number 4 / March, 2004 pp. 489-502
Generation of T-DNA Tagging Lines with a Bidirectional Gene Trap Vector and the Establishment of an Insertion-Site Database
Ryu et al.,
(1) National Research Laboratory of Plant Functional Genomics, Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, Republic of Korea
(2) Department of Molecular Biology, Pusan National University, Busan, 609-735, Republic of Korea
... been annotated in the public databases, we undertook annotation with the
Softberry program (http:// www.softberry.com/berry.phtml). ...
J Cell Biochem.
2004 Apr 1;91(5):1030-42
Characterizing the new transcription regulator protein p60T
Heese et al.,
BF Research Institute, c/o National Cardiovascular Center, 5-7-1 Fujishirodai, Suita, Osaka 565-0873, Japan
... expasy.ch): softberry: http://www.softberry. com/index.html; and Amino Acid Composition
Search (AACompIdent): http://kr.expasy.org/ tools/aacomp/. ...
Journal of Photoscience
2004, Vol. 11(3), pp. 115-120
Construction of Gene-Specific Primers for Various AntioxidantIsoenzyme Genes and Their Expressions in Rice (Oryza sativa L.)Seedlings Obtained from Gamma-irradiated Seed
Kim et al.,
1 Division of Radiation Application Research, Korea Atomic Energy Research Institute, Daejeon 305-353, Korea
... in the database (Table 1). In the case of CATa, its cDNA sequence was predicted
from the genomic DNA at a gene prediction site (http:// www.softberry.com/). ...
Genome Biol.
2003;5(1):R3. Epub 2003 Dec 22
An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome.
Hild et al.,
Zentrum fur Molekulare Biologie Heidelberg, University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
... Max Planck Institute for Molecular Genetics, Ihnestra?e 73, 14195 Berlin,
Germany. § Softberry, Inc., 116 Radio Circle, Suite ...
Invest Ophthalmol Vis Sci
2003;44: E-Abstract 418. 418—B393
Identification of Promoter and Other Regulatory Regions of Pitx3 Gene
E.V. Semina1, K. Frees2, S. Tomarev3, A. Cvekl4 and J.C. Murray4
1 Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
2 Pediatrics, University of Iowa, Iowa City, IA, United States
... MatInspector and Softberry software have been utilized to perform promoter searches
and to identify binding sites for transcription factors/potential ...
Physiological and Molecular Plant Pathology
Vol. 62, no. 5, pp. 305-313. May 2003
Characterisation of neutral trehalase and UDP-glucose:sterol glucosyltransferase genes from the plant pathogenic fungus Leptosphaeria maculans
Idnurm, A., Warnecke, DC., Heinz, E., Howlett, BJ.*
... The larger transcript, detected by amplification of cDNA using primers designed
within an exon predicted by DNA analysis software (www.softberry.com), encodes ...
Plant Physiology
133:2040-2047 (2003)
Generation and Analysis of End Sequence Database for T-DNA Tagging Lines in Rice
Suyoung An et al.,
National Research Laboratory of Plant Functional Genomics, Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea (S.A., S.P., D.-H.J., D.-Y.L., H.-G.K., J.-H.Y., J.H., S.-R.K., Y.-H.K., M.L., G.A.
... sequence had not yet been annotated in the public database, the sequence surrounding
the insertion site was annotated using the Softberry program (http://www ...
Plant Molecular Biology
Volume 52, Number 5 / July, 2003, pp. 923-934
Abundance of plastid DNA insertions in nuclear genomes of rice and Arabidopsis
Ilham A. Shahmuradov 1 , Yagut Yu. Akbarova 2, Victor V. Solovyev 3 and Jalal A. Aliyev 2
(1) Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
(2) Institute of Botany, Azerbaijan National Academy of Sciences, 370073 Baku, Azerbaijan
(3) Softberry Inc., 116 Radio Circle, Suite 400, Mount Kisco, NY 10549, USA
Nucleic Acids Research,
2003, Vol. 31, No. 4 1148-1155
Characterization of Arabidopsis thaliana ortholog of the human breast cancer susceptibility gene 1: AtBRCA1, strongly induced by gamma rays
S. Lafarge and M.-H. Montane*
CEA Cadarache, DSV-DEVM, Laboratoire de Radiobiologie Vegetale, Bat 185, F-13108 St Paul Lez Durance Cedex, France
...Gene structure prediction was done on software implemented on the Softberry web page (http://www.softberry.com/), analysis of protein domains using the SMART...
...The gene structure of At4g21070 was determined with three gene structure prediction software packages (Softberry, GenScan, Grail). .... To resolve this ambiguity in intron-exon prediction, we postulated the presence of two genes given by Softberry prediction software and performed northern blotting and 5' RACE to characterize the structural organization of the At4g21070 locus...
The Plant Cell
Vol. 14, 2107-2119, September 2002
Two Novel Fungal Virulence Genes Specifically Expressed in Appressoria of the Rice Blast Fungus
Chaoyang Xue a et al.,
a Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
... were sequenced and analyzed with several programs, including TRES (www.bioportal.
bic.nus.edu.sg/tres), Expasy (www.expasy.org), and SoftBerry (www.softberry.com ...
Biological Psychiatry
Volume 51, Issue 11, Pages 896-901
Association study of novel human serotonin 5-HT1B polymorphisms with alcohol dependence in taiwanese han
H.Sun et al.,
... be identified within the 5? regulatory region; however, sequence annotation using
the Nucleotide Sequence Analysis program (http://softberry.com/) predicts a ...
Journal of Bacteriology
January 2002, p. 183-190, Vol. 184, No. 1
Regulation of the acuF Gene, Encoding Phosphoenolpyruvate Carboxykinase in the Filamentous Fungus Aspergillus nidulans
Michael J. Hynes,* Oliver W. Draht,, and Meryl A. Davis
Department of Genetics, University of Melbourne, Parkville, Victoria 3010, Australia
... The Protein Sequence Analysis program (http://www.softberry.com/protein.html) predicted
a PEPCK (ATP) signature sequence between amino acids 275 and 290. ...
Eur J Neurosci.
2002 Jan;15(1):79-86.
Characterizing CGI-94 (comparative gene identification-94) which is down-regulated in the hippocampus of early stage Alzheimer's disease brain
Heese et al.,
BF Research Institute, c/o National Cardiovascular Center, 5-7-1 Fujishiro-dai, Suita, Osaka, 565-0873 Japan
... Additionally, protein sequence analysis was performed using the following programs
at ExPASy, http://www.expasy.ch; softberry, http://www/softberry.com/index ...
Plant Cell
2002 September; 14(9): 2107–2119.
doi: 10.1105/tpc.003426
Two Novel Fungal Virulence Genes Specifically Expressed in Appressoria of the Rice Blast Fungus
Chaoyang Xue et al.,
aDepartment of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
... were sequenced and analyzed with several programs, including TRES (www.bioportal.
bic.nus.edu.sg/tres), Expasy (www.expasy.org), and SoftBerry (www.softberry.com ...
Plant Physiol.
February 2002, Vol. 128, pp. 336-340
Cellulose Synthase-Like Genes of Rice
Samuel P. Hazen, John S. Scott-Craig, and Jonathan D. Walton
Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
... the corresponding proteins were deduced using gene prediction software from GeneMark
(Atlanta; http://opal.biology.gatech.edu/GeneMark) and Softberry, Inc. ...