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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

 (309)
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 gen […]

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

[…] zomev10), 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 f […]

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, RRID:SCR_0 […]

library_books

Draft genome of the Peruvian scallop Argopecten purpuratus

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

[…] Ensemble []. 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. T […]

library_books

A genome wide identification and comparative analysis of the lentil MLO genes

2018
PLoS One
PMCID: 5865747
PMID: 29570745
DOI: 10.1371/journal.pone.0194945

[…] g 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. The […]

library_books

The genomic and functional landscapes of developmental plasticity in the American cockroach

2018
Nat Commun
PMCID: 5861062
PMID: 29559629
DOI: 10.1038/s41467-018-03281-1

[…] rst de novo assembled preliminary contigs using idba v1.1.1 following default parameters. All protein-coding genes were then aligned to each set of contigs using genblastA v1.0.1 with “-e 1e-5 -r 1”. GeneWise v2.2.0 was finally utilized to predict the gene models in these two genomes, respectively, for each input seed of P. americana. Orthology across these blattodean species was analyzed as descr […]

Citations

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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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