An improved method for identifying functionally linked proteins using phylogenetic profiles.

ABSTRACT:

Background

Phylogenetic profiles record the occurrence of homologs of genes across fully sequenced organisms. Proteins with similar profiles are typically components of protein complexes or metabolic pathways. Various existing methods measure similarity between two profiles and, hence, the likelihood that the two proteins co-evolve. Some methods ignore phylogenetic relationships between organisms while others account for such with metrics that explicitly model the likelihood of two proteins co-evolving on a tree. The latter methods more sensitively detect co-evolving proteins, but at a significant computational cost. Here we propose a novel heuristic to improve phylogenetic profile analysis that accounts for phylogenetic relationships between genomes in a computationally efficient

SUBMITTER: Cokus S 

PROVIDER: S-EPMC1892086 | biostudies-literature | 2007 May

REPOSITORIES: biostudies-literature