Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species

Scipio is a tool based on the alignment program BLAT to determine the precise gene structure given a protein sequence and a genome sequence. It identifies intron-exon borders and splice sites and is able to cope with sequencing errors and genes spanning several contigs in genomes that have not yet been assembled to supercontigs or chromosomes. Instead of producing a set of hits with varying confidence, Scipio gives the user a coherent summary of locations on the genome that code for the query protein. The output contains information about discrepancies that may result from sequencing errors. Scipio has also successfully been used to find homologous genes in closely related species. Scipio was tested with 979 protein queries against 16 arthropod genomes (intra species search). For cross-species annotation, Scipio was used to annotate 40 genes from Homo sapiens in the primates Pongo pygmaeus abelii and Callithrix jacchus. The prediction quality of Scipio was tested in a comparative study against that of BLAT and the well established program Exonerate.Scipio is able to precisely map a protein query onto a genome. Even in cases when there are many sequencing errors, or when incomplete genome assemblies lead to hits that stretch across multiple target sequences, it very often provides the user with the correct determination of intron-exon borders and splice sites, showing an improved prediction accuracy compared to BLAT and Exonerate. Apart from being able to find genes in the genome that encode the query protein, Scipio can also be used to annotate genes in closely related species.In the post-genome era, sequence data is the entry point for many studies. Often, it is essential to obtain the correct genomic DNA sequences of eukaryotic genes because of the information contained in non-coding regions. For example, the intron regions contain important sites for the regulation of gene transcription, like enhancers, repressors, and silencers [1]. Transcription initiator seque