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BMCBI
2007

An improved method for identifying functionally linked proteins using phylogenetic profiles

8 years 7 months ago
An improved method for identifying functionally linked proteins using phylogenetic profiles
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 fashion. We first order the genomes within profiles and then enumerate runs of consecutive matches and accurately compute the probability of observing these. We hypothesize that profiles with many runs are ...
Shawn Cokus, Sayaka Mizutani, Matteo Pellegrini
Added 12 Dec 2010
Updated 12 Dec 2010
Type Journal
Year 2007
Where BMCBI
Authors Shawn Cokus, Sayaka Mizutani, Matteo Pellegrini
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