GeneWise pipeline

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

Download


Versioning


Add your version

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 IN pipelines

 (21)
2018
PMCID: 5893958
PMID: 29659813
DOI: 10.1093/gigascience/giy012

[…] homology searches against the black porgy genome with tblastn (version 2.2.19) [44]. we chose alignments with coverage >70% and identity >70% for further prediction of gene structures using genewise (version 2.2.0) [25]. finally, we obtained homologous sequences of 26 genes in the genome assembly of chinese black porgy (for more details, see table 3). all these predicted protein […]

2017
PMCID: 5397779
PMID: 28427344
DOI: 10.1186/s12864-017-3703-9

[…] in-paralogs with the best confidence values were selected as orthologous. the nucleotide sequences of each orthologous group were aligned to the predicted amino acid sequence of g. dybowskii using genewise 2-4-1 [26], followed by a series of customized perl scripts to extract the matched coding regions and to generate the proper alignment format for subsequent analyses. then, swamp 31-03-14 […]

2017
PMCID: 5570040
PMID: 28535200
DOI: 10.1093/gigascience/gix039

[…] l. vexillifer, o. niloticus, o. latipes, f. rubripes, and xenopus tropicalis were used as queries. we then predicted the structure of sequenced genes using the blast-hit sequence with the software genewise [52], extending in both 3΄ and 5΄ directions along the genome sequences. the results were further confirmed by non-redundant (nr) annotation. then the coding sequences from the start (atg) […]

2015
PMCID: 4400102
PMID: 25879221
DOI: 10.1371/journal.pbio.1002078

[…] kept. (2.) the gene regions identified in step 1 were extracted from the g. morsitans genome using a perl script. (3.) transcript sequences were obtained from the g. morsitans gene sequences, using genewise [59] with the respective d. melanogaster protein sequence., gene expression values for all d. melanogaster genes were obtained from the berkeley drosophila genome project […]

2015
PMCID: 4549895
PMID: 26306879
DOI: 10.1186/s13104-015-1371-x

[…] results were used to build draft gene models in a text editor. the dna sequences of putative gene regions were retrieved using the gbrowse tool and compared with ors that are closely related using genewise [57]. genewise allows the prediction of coding proteins based on similarity of translated dna and input protein sequence. putative ors inferred from genewise were aligned with known ant ors, […]

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

GeneWise reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GeneWise