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GeneWise specifications

Information


Unique identifier OMICS_11233
Name GeneWise
Interface Web user interface
Restrictions to use None
Input data A protein sequence and a genomic DNA sequence
Input format GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot
Computer skills Basic
Version 2.4.1
Stability Stable
Maintained Yes

Maintainer


  • person_outline Ewan Birney

Information


Unique identifier OMICS_11233
Name GeneWise
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A protein sequence and a genomic DNA sequence
Input format GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot
Operating system Unix/Linux
Computer skills Advanced
Version 2.4.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Ewan Birney

Publications for GeneWise

library_books

GeneWise and Genomewise.

2004 Genome Res
PMCID: 479130
PMID: 15123596
DOI: 10.1101/gr.1865504

GeneWise citations

 (497)
library_books

Chromosome scale assembly of the Monopterus genome

2018
GigaScience
PMCID: 5946948
PMID: 29688346
DOI: 10.1093/gigascience/giy046

[…] rubripes were downloaded from the ensemble platform [] (release 75) and aligned with the monopterus genome with the tblastn program []. 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 […]

library_books

The Gastrodia elata genome provides insights into plant adaptation to heterotrophy

2018
Nat Commun
PMCID: 5915607
PMID: 29691383
DOI: 10.1038/s41467-018-03423-5

[…] sorghum bicolor (phytozomev10) and zea mays (phytozomev10) were downloaded and mapped to the g. elata genome using tblastn (e-value ≤ 1e−5). the blast hits were conjoined by solar software. genewise (version 2.4.1) was used to predict the exact gene structure of the corresponding genomic region on each blast hit. homology predictions were denoted as “homology-set”. rna-seq data derived […]

library_books

Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes

2018
BMC Biol
PMCID: 5901865
PMID: 29661185
DOI: 10.1186/s12915-018-0509-4

[…] assemblathon_stats.pl [] developed by the assemblathon project []. cegma v2.5 [] referring to the cvg [] was utilized in order to assess the completeness of the assemblies. for the cegma runs, genewise v2.2.3-rc7 was employed []. busco v2.0.1 referring to its vertebrate gene set was further used for this purpose []., conventional and de novo repeat motifs in the p. picta genome assembly […]

library_books

Transcriptional Modulation of Human Endogenous Retroviruses in Primary CD4+ T Cells Following Vorinostat Treatment

2018
Front Immunol
PMCID: 5906534
PMID: 29706951
DOI: 10.3389/fimmu.2018.00603

[…] parameter, was estimated in edger by initially measuring a single dispersion parameter using all genes, while taking into account trends or gene abundances (i.e., trended dispersion). then genewise (i.e., tagwise) dispersion estimates are measured and an empirical bayes method was used to shrink these genewise dispersion estimates toward the trended dispersion. gene expression data […]

library_books

The draft genome sequence of forest musk deer (Moschus berezovskii)

2018
GigaScience
PMCID: 5906906
PMID: 29635287
DOI: 10.1093/gigascience/giy038

[…] 2.2.26) against the forest musk deer genome. potential gene regions were joined using solar (version 0.9.6) [], and the coding sequence with 500 bpflanking sequence was cut down and re-aligned using genewise (genewise, rrid:scr_015054) version 2.4.1 with parameters “- sum—genesf -gff” []. for transcriptome-based prediction, musk gland rna-seq data were assembled using trinity (trinity, […]

library_books

Draft genome of the Peruvian scallop Argopecten purpuratus

2018
GigaScience
PMCID: 5905365
PMID: 29617765
DOI: 10.1093/gigascience/giy031

[…] []. the protein sequences of homology species were aligned to the assembled genome with tblastn (basic local alignment search tool; e-value ≤10−5) [], and gene structures were predicted with genewise_2.4.1 (genewise, rrid:scr_015054) (the parameter set as “-genesf”) []. the transcriptome data were generated from adductor muscle, hepatopancreas, and mantle on illumina hiseq4000 platform. […]


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GeneWise institution(s)
The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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