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Bioinformatics Advance Access originally published online on May 5, 2007
Bioinformatics 2007 23(12):1468-1475; doi:10.1093/bioinformatics/btm133
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© 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, UK

*To whom correspondence should be addressed.


  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 into 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

Contact: alc{at}sanger.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Chris Stoeckert

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

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