Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score.

ABSTRACT:

Background

Identification of ortholog groups is a crucial step in comparative analysis of multiple genomes. Although several computational methods have been developed to create ortholog groups, most of those methods do not evaluate orthology at the sub-gene level. In our method for domain-level ortholog clustering, DomClust, proteins are split into domains on the basis of alignment boundaries identified by all-against-all pairwise comparison, but it often fails to determine appropriate boundaries.

Results

We developed a method to improve domain-level ortholog classification using multiple alignment information. This method is based on a scoring scheme, the domain-specific sum-of-pairs (DSP) score, which evaluates ortholog clustering results at the domain level as the sum tot

SUBMITTER: Chiba H 

PROVIDER: S-EPMC4035852 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature