Methods for incorporating the hypermutability of CpG dinucleotides in detecting natural selection operating at the amino acid sequence level.

ABSTRACT: In detecting natural selection operating at the amino acid sequence level by comparing the rates of synonymous (r(S)) and nonsynonymous (r(N)) substitutions, the rates of synonymous and nonsynonymous mutations are assumed to be approximately the same. In reality, however, these rates may not be the same if different proportions of synonymous and nonsynonymous sites overlap with CpG dinucleotides, which are known to be hypermutable in some organisms. Here, we develop the evolutionary pathway methods for comparing r(S) and r(N) at multiple codon sites (all-sites analysis) and at single codon sites (single-site analysis) that take into account the hypermutability at CpG dinucleotides in estimating the number of synonymous substitutions per synonymous site (d(S)) and nonsynonymous substitution

SUBMITTER: Suzuki Y 

PROVIDER: S-EPMC2766935 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature