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

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 approximately 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

SUBMITTER: Coghlan A 

PROVIDER: S-EPMC2880447 | biostudies-literature | 2007 Jun

REPOSITORIES: biostudies-literature