FOLLOWING IS AN ABBREVIATED RESULT OF SEARCH OF REPORTED USE OF SOFTBERRY
THROUGH ARTICLES IN SCIENCE AND NATURE JOURNALS
THE LAST YEARS.
Various Journal publications: Publications by topics and Publications by programs
Rinaldi, et al., (2016)
The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts.
Nature Communications 7, 8976. ... The complete mRNA transcript, including the TTE_RS07450 and TTE_RS07445 (TTE1564 and TTE1563, respectively) ORFs, and its 3? UTR as predicted from the
FindTerm algorithm (SoftBerry), was amplified using PCR from T. tengcongensis genomic DNA, which was purchased from the NITE Biological Resource Center. ...
Liu, et al., (2016)
The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts.
Nature Communications 7, 11757. ... AUGUSTUS and FGENESH (http://www.softberry.com) were used for genome annotation (Supplementary Fig. 4). ...
Mago, et al., (2015)
The wheat Sr50 gene reveals rich diversity at a cereal disease resistance locus.
Nature Plants 1, 15186. ... Reads were assembled using Newbler v2.3, wheat repeat sequences (http://wheat.pw.usda.gov/
ITMI/Repeats/blastrepeats3.html) masked and genes predicted using FGENESH
(www.softberry.com) and GENSCAN (http://genes.mit.edu/GENSCAN.html). ...
Wang, et al., (2015)
The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation.
Nature Genetics 47, 625-631 ... On the basis of the alignment results from steps 1-3, the target gene fragments found by extending the aligned regions by 3,000 bp on
both ends were selected to build preliminary gene models with FgeneSH++ (Softberry) using parameters trained on fish genomes. ...
Cai, et al., (2015)
The genome sequence of the orchid Phalaenopsis equestris.
Nature Genetics 47, 65-72. ... BESTORF was then used to predict ORFs with parameters trained on monocot genes without filtering out UTRs. ...
Kis-Papo, et al., (2014)
Genomic adaptations of the halophilic Dead Sea filamentous fungus Eurotium rubrum.
Nature Communications 5, 3745. ...The gene prediction methods were: transcriptome-based predictions with CombEST (http://genome.jgi.doe.gov/programs/fungi/combest.jsf) and ESTmap (http://softberry.com) using EST data comprising raw ESTs and assembled EST contigs; homology-based predictions with FGENESH+ (ref. 37) and Genewise38, with homology seeded by BLASTx alignments of the GenBank non-redundant sequence database (NR: http://www.ncbi.nlm.nih.gov/BLAST/) to the genomic scaffolds; and ab initio predictions using FGENESH pipeline34 and GeneMark39. ...
Takehana, et al., (2014)
Co-option of Sox3 as the male-determining factor on the Y chromosome in the fish Oryzias dancena.
Nature Communications 5, 4157. ... After assembly, gene annotation was performed using gene prediction software (GENSCAN; http://genes.mit.edu/GENSCAN.html and FGENESH; http://www.softberry.com/berry.phtml). ...
Bailey, et al., (2014)
Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population.
Nature Communications 5, 4076. ...Bent arrows indicate promoters predicted by the Softberry BPROM program (http://linux1.softberry.com/berry.phtml) ...
Dijkstra, et al., (2014)
TH2 and Treg candidate genes in elephant shark.
Nature 511 (7508), E7-E9. ...Genes without messenger RNA reports were predicted from genomic DNA sequences using GENSCAN (http://genes.mit.edu/GENSCAN.html) or FGENESH (http://linux1.softberry.com/berry ...
Moroz, et al., (2014)
The ctenophore genome and the evolutionary origins of neural systems.
Nature 510, 109-114. ...Three gene model predictions were performed by Augustus39 and Fgenesh predictions with the Softberry Inc.
Fgenesh++ pipeline 40, 41 ...
Lienard, et al., (2014)
Sex pheromone biosynthetic pathways are conserved between moths and the butterfly Bicyclus anynana.
Nature Communications 5, 3957. ...All scaffolds predicted to harbour desaturase and FAR-like genes were retrieved and annotated in Geneious Pro 5.6.4 (ref. 66);
intron-exon boundaries were predicted using tBLASTx, Softberry FGENESH and ExPasy prediction tools, manually curated and verified...
Tang, et al., (2014)
Genome of the human hookworm Necator americanus.
Nature Genetics 46, 261-269. ...Supplementary Information. A total of 19,151 genes were predicted by the following gene prediction algorithms: makeraugustus
(7,625), maker-snap (7,437), maker-genesh14 (1,309), augustus13 (2,656), snap12 (98),
fgenesh (www.softberry.com) (26)...
Lencz, et al., (2013) Genome-wide association study implicates NDST3 in schizophrenia and bipolar disorder. Nature Communications 4. ...TATA boxes were predicted by TSSG (Softberry Inc) and the predicted TATA box locations were depicted with vertical arrows (red on plus strand and blue on minus strand of chromosome 4) ...
Peng, et al., (2013) The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). Nature Genetics 45, 456-461. ...Protein-coding gene models were derived from evidence-based FgeneSH++ (Softberry) pseudomolecules (Supplementary Fig. 7). ...
Zhang, et al., (2012) Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nature Biotechnology 30 , 549-554. ...Open reading frames (ORFs) were predicted using BESTORF (http://linux1.softberry.com/berry.phtml?topic=bestorf&group=programs&subgroup=gfind) with parameters trained on monocot genes without filtering of UTRs. ...
O'Connell, et al., (2012) Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nature Genetics 44, 1060-1065. (Fgenesh)
Navarro, et al., (2011) Control of flowering and storage organ formation in potato by FLOWERING LOCUS T. Nature 478, 119-122. ... The best genome matches (Supplementary Table 2) were downloaded and open reading frames were predicted using FGENESH (http://linux1.softberry.com/berry.phtml) and ORF Finder ...
Deltcheva, et al., (2011) CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471, 602-607. ...Putative promoters were predicted using the BPROM software (http://www.softberry.com/) and BDGP Neural Network Promoter Prediction NNPP version 2.2...
Berka, et al., (2011) Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. Nature Biotechnology 29, 922-927. ... was performed using ab initio Fgenesh 32 and Genemark-ES 33 ; homology-based Fgenesh+ 32 and Genewise 34 seeded by BLASTx alignments of NCBI's nr (nonredundant) protein database against the assembly; cDNA-based EST_map (http://www.softberry.com/) seeded ...
Jex, et al., (2011) Ascaris suum draft genome. Nature 479, 522-523. ...The open reading frame of each gene was predicted using BestORF (http://www.softberry.com). ...
Dassanayake, et al., (2011) The genome of the extremophile crucifer Thellungiella parvula. Nature Genetics 43, 913-918. ...FGENESH++ (SoftBerry) was used to predict protein coding ORFs in the T. parvula draft genome masked for repetitive sequences, with parameters optimized for dicot plants and protein sequences from the NCBI non-redundant (NR) database as reference ...
Martin et al., (2009) A transposon-induced epigenetic change leads to sex determination in melon.
Nature 461, 1135-1138. ...After assembly, two forms of gene annotation were performed: (1) ab initio gene prediction with
GENSCAN (http://genes.mit.edu/GENSCAN.html), GeneMark.hmm (http://exon.gatech.edu/
GeneMark/eukhmm.cgi) and FGENESH (http://www.softberry.com/berry.phtml); ...
Bowler et al., (2008) The Phaeodactylum genome reveals the evolutionary history of diatom genomes.
Nature 4doi:10.1038/nature07410. ...Gene predictors used for these annotations included ab initio Fgenesh 12 trained on sets of known genes and reliable homology-based gene models from P. tricornutum and T.pseudonana, and homology-based Fgenesh+ 12 and Genewise 13 seeded by BLASTX alignments against sequences in the NCBI non-redundant protein set.. ...
Putnam et al., (2008) The amphioxus genome and the evolution of the chordate karyotype.
Nature 453, 1064 - 1071. ...Gene predictors used for annotation of amphioxus v1.0 included ab initio FGENESH 8, homology-based FGENESH+ 8, homology-based GENEWISE 9, and EST-based ESTEXT (Grigoriev, unpublished, available upon request). ...
Ming et al., (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).
Nature 452, 991 - 996. ...in training ab initio gene prediction software Augustus, GlimmerHMM and SNAP. Ab initio gene prediction software Fgenesh, Genscan and TWINSCAN were trained on Arabidopsis. Spliced alignments of proteins from the plant division of...
Richards et al., (2008) The genome of the model beetle and pest Tribolium castaneum.
Nature 452, 949 - 955. ...D. melanogaster shown in parentheses). Work at the BCM-HGSC was funded by grants from the NHGRI and USDA. FgenesH and FgenesH++ analysis was donated by Softberry Inc. This research was additionally supported in part by the Intramural...
Martin et al., (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis.
Nature 452, 88 - 92. ...in the scaffold assembly (Supplementary Table 2). Genome annotation Gene models were predicted using FgenesH, homology-based FgenesH+ (ref. 18) and Genewise, as well as EuGAne and TwinScan, and alignments of several complementary DNA...
Alexander Idnurm, Felicia J. Walton, Anna Floyd, Joseph Heitman. (2008) Identification of the sex genes in an early diverged fungus.
Nature 451, 193 - 196. ...were searched with BLASTp, BLASTn or tBLASTn programs. Gene predictions from unannotated genomic DNA were made with FGENESH software using the settings for Schizosaccharomyces pombe. HMG domains were aligned in ClustalW, in MacClade...
Chintapalli et al., (2007) Using FlyAtlas to identify better Drosophila melanogaster models of human disease.
Nature Genetics 39, 715 - 720. ....85% of probe sets against documented genes were found to be transcribed in at least one tissue; whereas 18%, 60% and 21% of HDP, sim4 and FGENESH features were ...
Shi et al., (2007) Embryo-specific silencing of a transporter reduces phytic acid content of maize and soybean seeds.
Nature Biotechnology 25, 930 - 937. ....A maize-trained version of the program FGENESH (Softberry) was used for prediction of potential protein-coding regions. ...
Jeffries et al., (2007) Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis.
Nature Biotechnology 25, 319 - 326. ...methods used for analysis of the P. stipitis genome include ab initio Fgenesh, homology-based Fgenesh+ (http://www.softberry.com/) and Genewise, and an EST-based method estExt (unpublished data). ...
Oliynyk et al., (2007) Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL23338 .
Nature Biotechnology 25, 447 - 453. ...Genome analysis and annotation. CDSs were predicted and annotated using the program fgenesB (http://www.softberry.com/), trained ab initio, and manually curated using Artemis (version 8) ...
Emanuelsson O., Brunak SA., Heijne G., Nielsen H. (2007) Locating proteins in the cell using TargetP, SignalP and related tools.
Nature Protocols 2, 953 - 971. ...SignalP 3.0, SignalP 2.0 and TargetP to PrediSi, Phobius and ProtComp 6.0 (a commercially available program from Softberry Inc.) on a set of exclusively mammalian proteins. ...
Mavromatis et al., (2007) Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.
Nature Methods 4, 495 - 500. ...We assembled sampled reads using three commonly used genome assemblers (Phrap, Arachne and JAZZ),
and predicted genes using two popular gene-finding pipelines (fgenesb and CRITICA/GLIMMER).... URLs. fgenesb: http://sun1.softberry.com/berry.phtml?topic=fgenesb&group=programs&subgroup=gfindb;
Kamper et al., (2006) Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis.
Nature 444, 97 - 101 Letter . ...These candidates were analysed with the integral prediction score of ProtComp 6.0 (http://www.softberry.com), yielding 426 candidate secreted proteins....
The Honeybee Genome Sequencing Consortium, (2006) Insights into social insects from the genome of the honey bee Apis mellifera.
Nature 433, 7114, 931-949. Using Fgenesh and Fgenesh++ pipeline for annotation of genes in the bee genome.
Martin et al., (2006) Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities.
Nature Biotechnology 24, 1263 - 1269. ... Over 30,000 coding sequences were predicted in each Phrap assembly using ab initio gene predictions (fgenesb, http://www.softberry.com/). ...
Frigaard et al., (2006) Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea.
Nature 439, 847-850. ...combined with sequence assembly with Sequencher v. 4.5 (Gene Codes Corporation) and annotation with FGENESB (Softberry) and Artemis v. 6 (The Wellcome Trust Sanger Institute). ...
Morgante et al., (2005) Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize.
Nature Genetics 37, 997-1002 Letters. ...We obtained FGENSH splicing site predictions from http://www.softberry.com/berry.phtml. Primer3 is available at http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi...
Dean et al. (2005) The genome sequence of the rice blast fungus Magnaporthe grisea.
Nature 434, 980-986. ...Gene predictions were performed using FGENESH/FGENESH1 + trained on M. grisea sequences (SoftBerry) and GENEWISE (Sanger Center) and validated against 65 characterized M. grisea genes. Additional information and gene identification...
Paine et al. (2005) Improving the nutritional value of Golden Rice through increased pro-vitamin A content.
Nature Biotechnology 23, 482-487 Research. ...genes identified genomic sequences of similarity in which genes were predicted using FGENESH algorithm with the monocot training set. Putative rice PSY sequences were...
Campbell, N (2005) Genomics: Closing the gap.
Nature Reviews Genetics 6, 160-160 Highlights. ...which were identified from either computer predictions (9,811 from GENSCAN and 375 from FGENESH) or microarray-based validation experiments (1,266). The authors then tested...
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome.
Nature 436, 793 - 800. ...Annotation and bioinformatics Gene models were predicted using FGENESH (http://www.softberry.com/berry.phtml?topic = fgenesh) using the monocot trained matrix on the native and repeat-masked...
Wang et al. (2004)
Mouse transcriptome: Neutral evolution of 'non-coding' complementary DNAs.
Nature 431, (2004) Brief Communications.
...'intergenic' sequences of 2 kb in length that are at least 5 kb distant from genes annotated by Ensembl, predicted by FGENESH, or aligned to cDNAs. Transposons identified by RepeatMasker are excluded, as is the 5% of highly......
Hashimoto et al. (2004)
5'-end SAGE for the analysis of transcriptional start sites.
Nature Biotechnology 22, 1146 - 1149. ...from expressed sequence tag (EST) maps, analysis of full-length cDNAs and computational annotation by Genscan, Genie, FGENES and other programs.
Ota et al. (2004)
Complete sequencing and characterization of 21,243 full-length human cDNAs.
Nature Genetics 36, 40 - 45
Grimwood J, Gordon LA, Olsen A, .., Solovyev V., ..., Lukas S. (2004)
The DNA sequence and biology of human chromosome 19. Nature
428(6982), 529-535. Using Fgenesh, Fgenesh+, est_map to annotate genes in Himan cjromosome 19.
Tyson, G.W., Chapman, J., Hugenholtz, P. , Allen, E. , Ram, R.J.*, Richardson, P., Solovyev, V., Rubin, E. , Rokhsar, D., and Banfield, J.F. (2004)
Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature
428(6978), 37-43. Using Softberry Bacterial_annotator automatic annotation pipele to annotate genes in Microbial community.
Steve Buckingham (2003)
Bioinformatics: Programmed for success.
Nature 425, 209 - 215 (11 Sep 2003) Technology Feature. ...Fast searching is also a feature of Genome Explorer from Softberry in Mount Kisco, New York, which uses the FMAP algorithm. This is a very fast algorithm developed by Softberry to map query sequence to large genomes. ...
Heiliget al. (2003)
The DNA sequence and analysis of human chromosome 14. Nature
421, 601 - 607. FGENESH used for human chromosome 14
et al. (2003)
The DNA sequence of human chromosome 7. Nature
424, 157 - 164. Extensive use of FGENESH-2 for human
chromosome 7 annotation.
et al. (2003)
The genome sequence of the filamentous fungus Neurospora
422:859-868. Neurospora genome annotation based on FGENESH
used for annotation of rice chromosome 4.
et al. (2002)
Sequence and analysis of rice chromosome 4. Nature
420, 316 - 320.
M. (2002) Putting a name on it. Nature
419, 755. Review of genefinding software.
et al. (2001)
Gene defect in ectodermal dysplasia implicates a death
domain adapter in development. Nature
414, 913 - 916. FGENESH use for prediction of genes in
human TNFR gene family.
et al. (2001)
Initial sequencing and analysis of the human genome. Nature
409, 860 - 921. Original paper on sequencing human genome
by public consortium also reports use of FGENESH
genefinder for genome annotation.
et al. (2001)
The DNA sequence and comparative analysis of human
chromosome 20. Nature 414, 865-871. Use of FGENESH for annotation of human
M.Q. (2002) Computational
prediction of eukaryotic protein-coding genes. Nature Reviews Genetics 3, 698 - 709. Review of gene prediction
Zhu, Fengyun; Tan, Xiaofeng; Chen, Hongpeng, (2012) A Novel Metallothionein Gene Putatively Related to Fatty Acid Biosynthesis in Camellia Oleifera Seeds Confronted to Heavy Metal Stress. Advanced Science Letters, Volume 10, Number 1, pp. 168-172(5) ...The sub-cellular location result predicted by Softberry revealed Co-MT deposit in cytoplasmid and it was a secreted protein. ...
Shao, Gongfeng; Tan, Xiaofeng; Chen, Hongpeng, (2012) Isolation and Characterization of An Aldo-Keto Reductase cDNA from Camellia Oleifera Seed. Advanced Science Letters, Volume 10, Number 1, pp. 153-157(5) ...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 ...
Tan, Xiaofeng; Chen, Hongpeng; Zhang, Dangquan; Hu, Fangming, (2012) A New Member of PAL Family Initiating Secondary Metabolism During Fatty Acid Biosynthesis in Camellia Oleifera Seeds. Advanced Science Letters, Volume 10, Number 1, pp. 191-195(5) ...The sub-cellular location result predicted by Softberry revealed Co-PAL deposit in cytoplasmid. ...
Han, Xiaoxia, et al., (2011) Cloning and Sequence Analysis of Candidate Disease Resistance Genes from Dongxiang Common Wild Rice (O. rufipogon Griff). Advanced Science Letters, Volume 4, Numbers 11-12, pp. 3653-3657(5). ... The Genomic DNA Sequence Analysis DNA sequence location and similarity analysis was performed by BLAST program (http://www.ncbi.nlm.nih.gov/).13 Gene pre- diction was performed by FGENESH (Solovyev and Salamov 1999; http://www.softberry.com/berry.phtml) and ...
The Nasonia Genome Working Group, (2010) Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species. Science 327, 343-348. (Fgenesh++, Fgenesh)
Schweitzer et al. (2009)
Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. canadensis.
Science 324: 626-631. ... The Anolis carolinensis amino acid sequence was inferred with the use
of FGENESH+ (gene prediction on the basis of protein homology; www.softberry.com). ...
Perez-Brocal et al. (2006)
A Small Microbial Genome: The End of a Long Symbiotic Relationship?
Science 314: 312-313. Fgenesb is used for gene annotation..
Julie C. Nemecek, Marcel W.thrich, and Bruce S. Klein (2006)
Global Control of Dimorphism and Virulence in Fungi.
Science 312: 583-588 [DOI: 10.1126/science.1124105] (in Reports). ... ORFA encodes a protein of 1274 residues (on the basis of transcript
size) and predicted by gene-finding software (Softberry, Mount Kisco, NY).
The gene has three exons totaling 3825 base pairs (bp) and two introns of
140 and 40 bp, and it displays...
Biology analysis group et al. (2004)
A Draft Sequence for the Genome of the Domesticated Silkworm (Bombyx mori).
Science 306: 1937-1940. Usage of FGENESH for gene finding.
Stolc et al. (2004)
A Gene Expression Map for the Euchromatic Genome of Drosophila melanogaster
Science 306: 655-660.
Usage of FGENESH++ pipeline for gene finding.
Ane et al. (2004)
Medicago truncatula DMI1 Required for Bacterial and Fungal Symbioses in Legumes.
Science 303: 1364-1367. Usage of FGENESH for gene finding.
Rice Chromosome 10 Sequencing Consortium (2003) In-Depth
View of Structure, Activity, and Evolution of Rice
Chromosome 10. Science 300: 1566-1569. Use
of FGENESH for annotation of rice chromosome 10.
et al. (2002) A
draft sequence of the rice genome (Oryza
sativa L. ssp. indica). Science
296:79-92. As part of rice genome sequencing project, the
team led by Beijing Genomics Institute has compared
several well-known ab initio gene prediction programs and
shown that FGENESH is by far the most accurate. As a
result, their rice genome annotation was based almost
exclusively on FGENESH results.
et al. (2002) A
draft sequence of the rice genome (Oryza
sativa L. ssp. japonica). Science
296:92-100 and supplement. Second rice genome sequencing
and annotation project also used FGENESH as primary source
of gene predictions.
et al. (2002)
The Genome Sequence of the Malaria Mosquito Anopheles
298: 129-149. Use of FGENESH for annotation of Anopheles
et al. (2002)
Activation of Orphan Receptors by the Hormone Relaxin. Science
295: 671-674. The authors used FGENES-M for prediction of
alternative gene sutructures.
et al. (2001)
The Sequence of the Human Genome. Science
291: 1304-1351. Original paper on sequencing human genome
by Celera, which reports
use of FGENESH genefinder for genome annotation.
D. (2001) Making Sense of the Sequence. Science
291: 1257-1260. Review of genome annotation programs that
includes Softberry genefinders.
& Nahon (2001) Birth of Two Chimeric Genes in the
Hominidae Lineage. Science
et al. (2000) A
Drosophila Mechanosensory Transduction Channel. Science
287: 2229-2234. Use of FGENESH for prediction of
Drosophila Ce-nompC gene structure.