Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes.

ABSTRACT: Ortholog identification is a crucial first step in comparative genomics. Here, we present a rapid method of ortholog grouping which is effective enough to allow the comparison of many genomes simultaneously. The method takes as input all-against-all similarity data and classifies genes based on the traditional hierarchical clustering algorithm UPGMA. In the course of clustering, the method detects domain fusion or fission events, and splits clusters into domains if required. The subsequent procedure splits the resulting trees such that intra-species paralogous genes are divided into different groups so as to create plausible orthologous groups. As a result, the procedure can split genes into the domains minimally required for ortholog grouping. The procedure, named DomClust, was tested usi

SUBMITTER: Uchiyama I 

PROVIDER: S-EPMC1351371 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature