Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment.

ABSTRACT:

Background

Accurate computational identification of eukaryotic gene organization is a long-standing problem. Despite the fundamental importance of precise annotation of genes encoded in newly sequenced genomes, the accuracy of predicted gene structures has not been critically evaluated, mostly due to the scarcity of proper assessment methods.

Results

We present a gene-structure-aware multiple sequence alignment method for gene prediction using amino acid sequences translated from homologous genes from many genomes. The approach provides rich information concerning the reliability of each predicted gene structure. We have also devised an iterative method that attempts to improve the structures of suspiciously predicted genes based on a spliced alignment algorithm using consen

SUBMITTER: Gotoh O 

PROVIDER: S-EPMC4065584 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature