Genome Res. 2004 May;14(5):988-95.

GeneWise and Genomewise.

Source

The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. birney@ebi.ac.uk

Abstract

We present two algorithms in this paper: GeneWise, which predicts gene structure using similar protein sequences, and Genomewise, which provides a gene structure final parse across cDNA- and EST-defined spliced structure. Both algorithms are heavily used by the Ensembl annotation system. The GeneWise algorithm was developed from a principled combination of hidden Markov models (HMMs). Both algorithms are highly accurate and can provide both accurate and complete gene structures when used with the correct evidence.

PMID:: 15123596; [PubMed - indexed for MEDLINE]
PMCID: PMC479130

Free PMC Article

Images from this publication.See all images (3) Free text

Publication Types, MeSH Terms, Substances

Publication Types

MeSH Terms

Substances

DNA, Complementary

LinkOut - more resources

Full Text Sources

Other Literature Sources

Labome Researcher Resource - ExactAntigen/Labome

Supplemental Content

Related citations

[Analysis, identification and correction of some errors of model refseqs appeared in NCBI Human Gene Database by in silico cloning and experimental verification of novel human genes]. [Yi Chuan Xue Bao. 2004]
[Analysis, identification and correction of some errors of model refseqs appeared in NCBI Human Gene Database by in silico cloning and experimental verification of novel human genes].
Zhang DL, Ji L, Li YD. Yi Chuan Xue Bao. 2004 May; 31(5):431-43.
Pairagon+N-SCAN_EST: a model-based gene annotation pipeline. [Genome Biol. 2006]
Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.
Arumugam M, Wei C, Brown RH, Brent MR. Genome Biol. 2006; 7 Suppl 1:S5.1-10. Epub 2006 Aug 7.
The identification of complete domains within protein sequences using accurate E-values for semi-global alignment. [Nucleic Acids Res. 2007]
The identification of complete domains within protein sequences using accurate E-values for semi-global alignment.
Kann MG, Sheetlin SL, Park Y, Bryant SH, Spouge JL. Nucleic Acids Res. 2007; 35(14):4678-85. Epub 2007 Jun 27.
JIGSAW: integration of multiple sources of evidence for gene prediction. [Bioinformatics. 2005]
JIGSAW: integration of multiple sources of evidence for gene prediction.
Allen JE, Salzberg SL. Bioinformatics. 2005 Sep 15; 21(18):3596-603. Epub 2005 Aug 2.
Review Computational approaches to gene prediction. [J Microbiol. 2006]
Review Computational approaches to gene prediction.
Do JH, Choi DK. J Microbiol. 2006 Apr; 44(2):137-44.

See reviews... See all...

Cited by over 100 PubMed Central articles

Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data. [PLoS One. 2012]
Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data.
Hartmann S, Helm C, Nickel B, Meyer M, Struck TH, Tiedemann R, Selbig J, Bleidorn C. PLoS One. 2012; 7(1):e29843. Epub 2012 Jan 20.
Genome comparison of human and non-human malaria parasites reveals species subset-specific genes potentially linked to human disease. [PLoS Comput Biol. 2011]
Genome comparison of human and non-human malaria parasites reveals species subset-specific genes potentially linked to human disease.
Frech C, Chen N. PLoS Comput Biol. 2011 Dec; 7(12):e1002320. Epub 2011 Dec 22.
Gene decay in Shigella as an incipient stage of host-adaptation. [PLoS One. 2011]
Gene decay in Shigella as an incipient stage of host-adaptation.
Feng Y, Chen Z, Liu SL. PLoS One. 2011; 6(11):e27754. Epub 2011 Nov 16.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

GeneWise and Genomewise.
GeneWise and Genomewise.
Genome Res. 2004 May ;14(5):988-95.

PubMed
Improving the Arabidopsis genome annotation using maximal transcript alignment a...
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.
Nucleic Acids Res. 2003 Oct 1 ;31(19):5654-66.

PubMed
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic s...
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Nucleic Acids Res. 1997 Mar 1 ;25(5):955-64.

PubMed
Update in idiopathic pulmonary fibrosis.
Update in idiopathic pulmonary fibrosis.
Curr Opin Pulm Med. 2009 Sep ;15(5):463-9.

PubMed
Comparison of necropsy findings in patients with sarcoidosis dying suddenly from...
Comparison of necropsy findings in patients with sarcoidosis dying suddenly from cardiac sarcoidosis versus dying suddenly from other causes.
Am J Cardiol. 2009 Aug 15 ;104(4):571-7. Epub 2009 Jun 18 .

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to: