Skip Navigation


Bioinformatics Advance Access first published online on May 5, 2007
This version published online on May 5, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm133
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary data
Right arrowOA All Versions of this Article:
23/12/1468    most recent
btm133v2
btm133v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Coghlan, A.
Right arrow Articles by Durbin, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Coghlan, A.
Right arrow Articles by Durbin, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomix: a method for combining gene-finders’ predictions, which uses evolutionary conservation of sequence and intron-exon structure

Avril Coghlan and Richard Durbin *

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, United Kingdom

*To whom correspondence should be addressed. Richard Durbin, E-mail: rd{at}sanger.ac.uk


  Abstract

Motivation: Correct gene predictions are crucial for most analyses of genomes. However, in the absence of transcript data, gene prediction is still challenging. One way to improve gene-finding accuracy in such genomes is to combine the exons predicted by several gene-finders, so that gene-finders that make uncorrelated errors can correct each other.

Results: We present a method for combining gene-finders called Genomix. Genomix selects the predicted exons that are best conserved within and/or between species in terms of sequence and intron-exon structure, and combines them intgo a gene structure. Genomix was used to combine predictions from four gene-finders for Caenorhabditis elegans, by selecting the predicted exons that are best conserved with C. briggsae and C. remanei. On a set of ~1500 confirmed C. elegans genes, Genomix increased the exon-level specificity by 10.1% and sensitivity by 2.7% compared to the best input gene-finder.

Availability: Scripts and supplementary material can be found at {{http://www.sanger.ac.uk/Software/analysis/genomix}}.

Supplementary Information: Supplementary data are available at Bioinformatics online.

Associate Editor: Dr. Chris Stoeckert

Received on January 29, 2007; revised on March 28, 2007; accepted on March 30, 2007

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
S. D'Aniello, M. Irimia, I. Maeso, J. Pascual-Anaya, S. Jimenez-Delgado, S. Bertrand, and J. Garcia-Fernandez
Gene Expansion and Retention Leads to a Diverse Tyrosine Kinase Superfamily in Amphioxus
Mol. Biol. Evol., September 1, 2008; 25(9): 1841 - 1854.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Irimia and S. W. Roy
Spliceosomal introns as tools for genomic and evolutionary analysis
Nucleic Acids Res., March 1, 2008; 36(5): 1703 - 1712.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.