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

ABSTRACT:

Background

For many types of analyses, data about gene structure and locations of non-coding regions of genes are required. Although a vast amount of genomic sequence data is available, precise annotation of genes is lacking behind. Finding the corresponding gene of a given protein sequence by means of conventional tools is error prone, and cannot be completed without manual inspection, which is time consuming and requires considerable experience.

Results

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 supercon

SUBMITTER: Keller O 

PROVIDER: S-EPMC2442105 | biostudies-literature | 2008 Jun

REPOSITORIES: biostudies-literature