Ancient evolutionary signals of protein-coding sequences allow the discovery of new genes in the Drosophila melanogaster genome

BACKGROUND: The current growth in DNA sequencing techniques makes of genome annotation a crucial task in the genomic era. Traditional gene finders focus on protein-coding sequences, but they are far from being exhaustive. The number of this kind of genes continuously increases due to new experimental data and development of improved bioinformatics algorithms. RESULTS: In this context, AnABlast represents a novel in silico strategy, based on the accumulation of short evolutionary signals identified by protein sequence alignments of low score. This strategy potentially highlights protein-coding regions in genomic sequences regardless of traditional homology or translation signatures. Here, we analyze the evolutionary information that the accumulation of these short signals encloses. Using the Drosophila melanogaster genome, we stablish optimal parameters for the accurate gene prediction with AnABlast and show that this new strategy significantly contributes to add genes, exons and pseudogenes regions, yet to be discovered in both already annotated and new genomes. CONCLUSIONS: AnABlast can be freely used to analyze genomic regions of whole genomes where it contributes to complete the previous annotation.