GeneWise protocols

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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

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GeneWise and Genomewise.

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

GeneWise in pipelines

 (59)
2018
PMCID: 5865747
PMID: 29570745
DOI: 10.1371/journal.pone.0194945

[…] soybean [] and medicago [] mlo protein sequences as query were carried out to identify additional scaffolds containing the homologous lentil genes. coding dna regions (cds) were annotated using the genewise tool []. the deduced lentil protein sequences were validated by reciprocal blast searches carried out on the protein ncbi datasets of the m. truncatula, chickpea, and common bean genomes. […]

2018
PMCID: 5893958
PMID: 29659813
DOI: 10.1093/gigascience/giy012

[…] for homology searches against the black porgy genome with tblastn (version 2.2.19) []. we chose alignments with coverage >70% and identity >70% for further prediction of gene structures using genewise (version 2.2.0) []. finally, we obtained homologous sequences of 26 genes in the genome assembly of chinese black porgy (for more details, see table ). all these predicted protein sequences […]

2017
PMCID: 5357004
PMID: 28306751
DOI: 10.1371/journal.pone.0172966

[…] same numbers of cysteine with the same spacing. each msa was then used to build an hmm profile using hmmer (3.0) []. this gave rise to a library of 143 profiles. the profile library was used through genewise [] to directly scan the contigs, bypassing the translation step. all the identified contigs were submitted to a selective step to remove those that diverged from canonical sequences due […]

2017
PMCID: 5428418
PMID: 28331183
DOI: 10.1038/s41598-017-00403-5

[…] litura (identified in the previous step) were used as queries to perform tblastn search to identify putative csp coding regions. for such region, homology-based gene prediction was performed using genewise v2.2.0 with the most similar query sequence as reference. all predicted genes were further examined for the presence of the characteristic csp domain in their translated protein sequences. […]

2017
PMCID: 5450542
PMID: 28492509
DOI: 10.3390/md15050136

[…] testing correction outcomes [], using the bioconductor packages genefilter v1.46.1 [] and deseq v1.16.0 [] as described in the genefilter vignette []. the bottom 50% of genes, as ranked by total genewise counts across samples, were removed accordingly. differential gene expression (dge) analysis was performed using edger version 3.6.8 [,,,]. to help compensate for the lack of available […]


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GeneWise in publications

 (474)
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 […]

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 […]

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 […]

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 […]

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, […]


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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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