Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix.

ABSTRACT:

Background

Selective pressures at the DNA level shape genes into profiles consisting of patterns of rapidly evolving sites and sites withstanding change. These profiles remain detectable even when protein sequences become extensively diverged. A common task in molecular biology is to infer functional, structural or evolutionary relationships by querying a database using an algorithm. However, problems arise when sequence similarity is low. This study presents an algorithm that uses the evolutionary rate at codon sites, the dN/dS (ω) parameter, coupled to a substitution matrix as an alignment metric for detecting distantly related proteins. The algorithm, called BLOSUM-FIRE couples a newer and improved version of the original FIRE (Functional Inference using Rates of Evolution) algo

SUBMITTER: Ndhlovu A 

PROVIDER: S-EPMC4535666 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature