MACHOS: Markov clusters of homologous subsequences.

ABSTRACT:

Motivation

The classification of proteins into homologous groups (families) allows their structure and function to be analysed and compared in an evolutionary context. The modular nature of eukaryotic proteins presents a considerable challenge to the delineation of families, as different local regions within a single protein may share common ancestry with distinct, even mutually exclusive, sets of homologs, thereby creating an intricate web of homologous relationships if full-length sequences are taken as the unit of evolution. We attempt to disentangle this web by developing a fully automated pipeline to delineate protein subsequences that represent sensible units for homology inference, and clustering them into putatively homologous families using the Markov clustering algorithm.

SUBMITTER: Wong S 

PROVIDER: S-EPMC2718622 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature