GeneWise specifications

Information


Unique identifier OMICS_11233
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
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 <>

GeneWise articles

GeneWise citations

 (8)
2016
PMCID: 4881053

[…] threshold e value of 1e-5. the outputs in m8 format were extracted and only the best hits were selected for structural analyses. based on the best hits, r-gene structures were re-annotated using the genewise software [50]. the different structures of the r-genes were identified, such as open-reading frame shift, premature stop codon mutations, or insertion/deletions. additional file 3: figure s2 […]

2015
PMCID: 4549895

[…] 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, and problem […]

2015
PMCID: 4400102

[…] genes were located on the genomes of each outgroup species by mapping d. melanogaster coding sequences with blat [56] (with a translated query and database, and keeping only reciprocal best hits). genewise was then used on these homologous dna segments (using the d. melanogaster protein sequence as input) to obtain protein-coding sequences for each of them., protein sequences of genes […]

2012
PMCID: 3343110

[…] in the dataset. probability density functions for the microarray data were generated by kernel density estimation in r., close relatives of mmervk10c were found by using mmervk10c as a template for genewise [70] to predict pol and pro sequences in the repbase database of repetitive dna sequences [3]. multiple protein alignment was performed using clustalw [71], and phylogenetic trees […]

2010
PMCID: 2886108

[…] all models were transferred as expected due to small sequence variation resulting from a new, independent assembly. in a second mapping round, unmapped genes were aligned to the new assembly using genewise [12] an algorithm that combines protein alignment and gene prediction into a single statistical model as a paired hidden markov model (hmm) and provides a gene prediction based on protein […]

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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