A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches.

ABSTRACT:

Motivation

Identifying orthologous genes in multiple genomes is a fundamental task in comparative genomics. Construction of intergenomic symmetrical best matches (SymBets) and joining them into clusters is a popular method of ortholog definition, embodied in several software programs. Despite their wide use, the computational complexity of these programs has not been thoroughly examined.

Results

In this work, we show that in the standard approach of iteration through all triangles of SymBets, the memory scales with at least the number of these triangles, O(g(3)) (where g = number of genomes), and construction time scales with the iteration through each pair, i.e. O(g(6)). We propose the EdgeSearch algorithm that iterates over edges in the SymBet graph rather than triangles o

SUBMITTER: Kristensen DM 

PROVIDER: S-EPMC2881409 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature