Computing Ka and Ks with a consideration of unequal transitional substitutions.

ABSTRACT:

Background

Approximate methods for estimating nonsynonymous and synonymous substitution rates (Ka and Ks) among protein-coding sequences have adopted different mutation (substitution) models. In the past two decades, several methods have been proposed but they have not considered unequal transitional substitutions (between the two purines, A and G, or the two pyrimidines, T and C) that become apparent when sequences data to be compared are vast and significantly diverged.

Results

We propose a new method (MYN), a modified version of the Yang-Nielsen algorithm (YN), for evolutionary analysis of protein-coding sequences in general. MYN adopts the Tamura-Nei Model that considers the difference among rates of transitional and transversional substitutions as well as factors in cod

SUBMITTER: Zhang Z 

PROVIDER: S-EPMC1552089 | biostudies-literature | 2006 Jun

REPOSITORIES: biostudies-literature