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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 citations

 (388)
library_books

Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici)

2018
PLoS One
PMCID: 5927432
PMID: 29709017
DOI: 10.1371/journal.pone.0193922

[…] ts 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 InteractionThe molecular docking analysis of WRKY domain from Soly […]

library_books

De Novo DNA Synthesis in Aedes aegypti Midgut Cells as a Complementary Strategy to Limit Dengue Viral Replication

2018
Front Microbiol
PMCID: 5932203
PMID: 29755433
DOI: 10.3389/fmicb.2018.00801

[…] (Slater 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., ). […]

library_books

The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides

2018
Sci Rep
PMCID: 5916904
PMID: 29695739
DOI: 10.1038/s41598-018-24939-2

[…] s 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, P. […]

library_books

Chromosome scale assembly of the Monopterus genome

2018
GigaScience
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 refer […]

library_books

Inter genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum

2018
BMC Genomics
PMCID: 5907747
PMID: 29673315
DOI: 10.1186/s12864-018-4612-2

[…] asker (version 4.0.5) []. A F. venenatum specific repeat library was constructed using RepeatModeler (version 1.0.7) and supplied to MAKER for the repeat masking step. Gene calls were generated using FGENESH (version 3.1.2) [] using the Fusarium matrix, AUGUSTUS (version 2.7) [] using F. graminearum species model, GeneMark [] and SNAP [], with evidence taking Fusarium reviewed proteins in UNIPROT […]

library_books

Evolution of structural diversity of trichothecenes, a family of toxins produced by plant pathogenic and entomopathogenic fungi

2018
PLoS Pathog
PMCID: 5897003
PMID: 29649280
DOI: 10.1371/journal.ppat.1006946

[…] (New England BioLabs).Sequence reads obtained from each platform were processed and assembled using CLC Genomics Workbench (Qiagen Inc.). Gene predictions were done using the program Augustus [] and FGENESH (Softberry, Inc., Mount Kisco, New York). All TRI and housekeeping genes obtained from the genome sequences and used in phylogenetic analyses were also manually annotated. The 18 TRI genes use […]

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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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