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

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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@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.