FGENES protocols

View FGENES computational protocol

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FGENES specifications

Information


Unique identifier OMICS_25586
Name FGENES
Interface Web user interface
Restrictions to use None
Input data A nucleotide sequence.
Input format FASTA
Computer skills Basic
Version 1.5
Maintained Yes

Additional information


http://www.softberry.com/berry.phtml?topic=fgenes&group=help&subgroup=gfind

FGENES in pipelines

 (2)
2014
PMCID: 3890534
PMID: 24405787
DOI: 10.1186/1471-2164-15-14

[…] the thermal stress, acid stress and control conditions (table )., 2 m- osmotic stress; 50°c– thermal stress; ph- acid stress and control-no stress., the automatic annotation of the genome using the fgenes software (http://www.softberry.com), followed by manual curation of the c. pseudotuberculosis strain 1002 genome, identified 2,090 coding regions. from the cdna sequencing performed using […]

2007
PMCID: 2216076
PMID: 17850661
DOI: 10.1186/bcr1765

[…] as determined through medgene database searches with terms carcinoma, ductal breast carcinoma, neoplasms and breast neoplasms). dgenes involved in 'development', egenes involved in morphogenesis and fgenes involved in the cell cycle, as functionally annotated by the david database and contributed to the enrichment probability calculations – these three major gene ontology biological processes […]


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FGENES in publications

 (10)
PMCID: 5447745
PMID: 28611814
DOI: 10.3389/fpls.2017.00902

[…] , http://helix.wustl.edu/dcaps/dcaps.html , http://blast.ncbi.nlm.nih.gov/blast.cgi/ , http://cuke.vcru.wisc.edu/wenglab/ , http://www.softberry.com/berry.phtml?topic=fgenes_plus&group=programs&subgroup=gfs , http://www.softberry.com/berry.phtml?topic=index\&group=programs\&subgroup=gfind , https://melonomics.net/files/genome/melon_genome_v3.5.1/ […]

PMCID: 4994961
PMID: 27551866
DOI: 10.1371/journal.pone.0160945

[…] the intron and exon organizations and predicted protein locations of the vpes were analyzed using fgenesh-c (http://linux1.softberry.com/berryphtml?topic=fgenes_c&group=programs&subgroup=gfs)., multiple sequence alignment analysis of the putative amino acid sequences of 6 grapevine vpes and 4 arabidopsis thaliana vpes was performed using […]

PMCID: 4652430
PMID: 26581393
DOI: 10.1186/s12864-015-2190-0

[…] v1.0.2 with rfam v10.0 based on their homologies to known ncrna sequences.table 2 aprotein coding sequence bribosomal rna ctransfer rna dnon coding rna enon-pathogenic; received as pv. barbareae fgenes predicted using both genomic and rna sequencing (rnaseq) datasets, aprotein coding sequence, bribosomal rna, ctransfer rna, dnon coding rna, enon-pathogenic; received as pv. barbareae , […]

PMCID: 4509610
PMID: 26193888
DOI: 10.1186/s12863-015-0241-9

[…] validated snps are in bold c maf minor allele frequency d σ a2 = additive variance; σ p2 = phenotypic variance egenes with both top snps in discovery and validation inside them are in bold fgenes with individually validated snps within them, abtc: bos taurus chromosome, bintervals containing individually validated snps are in bold, c maf minor allele frequency, d σ a2 = additive […]

PMCID: 4524475
PMID: 26019165
DOI: 10.1093/gbe/evv094

[…] against the draft genomes in brig. prophage regions were identified in the draft genomes using phast (). following manual checking and examination, novel prophage regions were reannotated using fgenes (softberry inc., usa). annotation of cdss was based on results of aa sequence searches against the pfam database (accessed at http://pfam.xfam.org/) and using blastp against the ncbi nr […]


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