FGENESH pipeline

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

 (41)
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 states1) were used to identify the untranslated regions (utrs), exons, and introns within the scaffold containing sequences of chosen […]

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

[…] 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 states1) were used to identify the untranslated regions (utrs), exons, and introns within the scaffold containing sequences of chosen tobacco genes, […]

2018
PMCID: 5877630
PMID: 29517986
DOI: 10.3390/ijms19030769

[…] the candidate sweet genes were subsequently aligned. meanwhile, inconsistencies in the sequence alignment were resolved and absent sequences were predicted using fgenesh software [51] and cloned to determine the complete sequences. the g. raimondii [33] and g. arboreum [40] sweet genes were identified using similar methods., the sweet genes were named […]

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 epichloĆ« festucae were the fgenesh gene predictions previously used in the clavicipitaceae analysis [135]. putative orthologs were identified by using two methods. the first method was application of ortho-mcl and coco-cl […]

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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