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FGENESH specifications

Information


Unique identifier OMICS_01483
Name FGENESH
Interface Web user interface
Restrictions to use None
Input data A nucleotide sequence.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Victor Solovyev <>

Publication for FGENESH

FGENESH in pipelines

 (89)
2018
PMCID: 5820362
PMID: 29503658
DOI: 10.3389/fpls.2018.00185

[…] were returned by aat package)., in parallel, the ncbi database was used for blastn searches of nicotiana sequences with homology to the already annotated a. thaliana sequences of metal transporters. fgenesh and fgenesh+ tools (softberry, mount kisco, ny, united states) were used to identify the untranslated regions (utrs), exons, and introns within the scaffold containing sequences of chosen […]

2018
PMCID: 5897749
PMID: 29681911
DOI: 10.3389/fpls.2018.00432

[…] join map 4.0 with a lod threshold score of 3.0. the pcr reaction and gel electrophoresis was conducted as described in ., candidate genes in target region were predicted using the online program fgenesh and the cucumber genome database () and their annotations were obtained with the blastp tool from ncbi. for the candidate gene identified, the dna, cdna and protein sequences alignments […]

2018
PMCID: 5940169
PMID: 29599177
DOI: 10.1534/g3.118.200201

[…] we manually tested on the genome assembly (using ensembl blastn method with the closest ortholog as query) whether this was due to gene loss or annotation skews. in the latter case, we used the fgenesh+ program of the softberry suite (http://www.softberry.com/) to extract the gene sequence and predict the protein sequence., sequence alignments were performed using clustal omega v1.2.1 () […]

2017
PMCID: 5225507
PMID: 28073340
DOI: 10.1186/s12864-016-3457-9

[…] joint genome institute (trichoderma reesei, c. falcatum, c. somersetensis, c. caudatum, c. eremochloae, c. zoysiae, c. sublineola strain s3.001). protein sequences from epichloë festucae were the fgenesh gene predictions previously used in the clavicipitaceae analysis []. putative orthologs were identified by using two methods. the first method was application of ortho-mcl and coco-cl […]

2017
PMCID: 5419654
PMID: 28475636
DOI: 10.1371/journal.pone.0177061

[…] of wheat chromosome 4as-4al []., predictions of coding sequences (cds) and protein sequences were obtained for each of the tanaat1, tanaat2 and tadmas1 genes using the gene prediction software fgenesh. the coding sequences of all tanaat1, tanaat2 and tadmas1 genes were then validated using blastn searches to the tgacv1 genome assembly […]


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FGENESH in publications

 (581)
PMCID: 5945835
PMID: 29780401
DOI: 10.3389/fpls.2018.00608

[…] et al., unpublished data 2017) with the parameter “-evalue 1e-5”. then, the candidate contigs identified by tblastn (supplementary table ) were used to predict the gene models of blspls using the fgenesh online tool with the genome-specific gene-finding parameters of a. thaliana and p. trichocarpa (softberry, http://www.softberry.com/berry.phtml; solovyev et al., ). all the nonredundant gene […]

PMCID: 5927432
PMID: 29709017
DOI: 10.1371/journal.pone.0193922

[…] revealed the homologous sequences (babp01013778.1: having the sequence identity 84% and the query coverages 96%) and were retrieved into the positive frame through the reverse complementation. the fgenesh programme (http://www.softberry.com/) was used to find out coding sequences, transcriptional start, and end sites., dna-protein interaction, the molecular docking analysis of wrky domain […]

PMCID: 5932203
PMID: 29755433
DOI: 10.3389/fmicb.2018.00801

[…] et al., ). reverse translation allowed us to find the genome coordinates of hnt. the complete genomic region was screened for coding-sequences (cds) using mrna prediction tools like augustus, fgenesh, geneid, genemark, and genscan (burge and karlin, ; salamov and solovyev, ; besemer and borodovsky, ; blanco et al., ; keller et al., )., the sequences of hnt and mammal orthologue ras […]

PMCID: 5916904
PMID: 29695739
DOI: 10.1038/s41598-018-24939-2

[…] in the genome. first, the genome was repeat masked using the result of repeat annotation. then the masked genome was fed to the maker2 pipeline with the ab initio gene predictors being genemark-es, fgenesh, augustus and snap. and for the evidence-driven gene prediction, cdna of p. infestans and proteins of six related species from ensembl (release-28, p. infestans, p. kernoviae, p. lateralis, […]

PMCID: 5946948
PMID: 29688346
DOI: 10.1093/gigascience/giy046

[…] accordingly, homologous genomic sequences were input into the genewise program [] to align matching proteins. this procedure allowed us to define gene structures. for de novo prediction, both the fgenesh [] and genscan [] programs were used to predict coding genes with the appropriate parameters. homology-based and de novo- derived gene sets were combined with comprehensive, nonredundant […]


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FGENESH institution(s)
Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, UK; Softberry Inc., Mount Kisco, NY, USA

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