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 <>

FGENESH article

FGENESH citations

 (19)
2017
PMCID: 5727091

[…] alignment program (http://www.ebi.ac.uk/tools/msa/mafft/). the sequence alignments were illustrated using the jalview tool (waterhouse et al., 2009)., gene predictions were performed with the fgenesh tool (solovyev et al., 2006). the predicted protein sequences from the pmr1 region were blastp searched against the ncbi database for disease resistance-related genes. protein domain analysis […]

2017
PMCID: 5680213

[…] and s. polychroa. we identified sequences producing a significant alignment with the genes of interest. the top blast hit was used to predict smed-ache, pto-ache, pte-ache, dl-ache and sp-ache via fgenesh+ (http://www.softberry.com/). homology at the protein level between predicted smed-ache and hs-ache was analyzed using blast., the previous predicted sequences were used as template for blast […]

2016
PMCID: 5176316

[…] databases using the in-built blast (basic local alignment search tool) function., gene structure of putative resistance genes in the bac clone assembly was identified using gene prediction software fgenesh (softberry, mount kisco, ny, usa). pcr primers covering the protein-coding regions of predicted genes were designed with the software primer3plus (dr. andreas untergasser, michelstadt, […]

2016
PMCID: 4987456

[…] gene. all primers used in this work were designed with primer premier 5.0 (http://www.premierbiosoft.com/primerdesign/). open reading frames were further analyzed using the gene prediction program fgenesh (softberry inc., mount kisco, ny, usa). protein domain and motif predictions were performed with smart software (http://smart.embl-heidelberg.de/). the ste7 protein sequences from different […]

2016
PMCID: 5103229

[…] inversion of wheat chromosome 4as‐4al (liu et al., 1992)., gene prediction models including predicted cds and protein sequence were obtained for each of the identified tanas genes using fgenesh software (http://www.softberry.com). cds alignments (clustalw) and protein alignments based on the degree of amino acid conservation (clustalw—cost matrix blosum62, threshold 1) […]

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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