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


BACKGROUND
Scripts and Supplementary Material can be found at http://www.sanger.ac.uk/Software/analysis/genomix
Coghlan
Avril
A
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. alc@sanger.ac.uk
Durbin
Richard
R
D000818:Animals; D001483:Base Sequence; D002107:Caenorhabditis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D004247:DNA / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D005091:Exons; D049751:Genome, Helminth; D007438:Introns; D008957:Models, Genetic; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software
D021901:DNA, Intergenic; D004247:DNA