Selective constraints on amino acids estimated by a mechanistic codon substitution model with multiple nucleotide changes.

ABSTRACT:

Background

Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code, and the strength of selective constraints against amino acid replacements can be tailored to a given gene. First, selective constraints averaged over proteins are estimated by maximizing the likelihood of each 1-PAM matrix of empirical amino acid (JTT, WAG, and LG) and codon (KHG) substitution matrices. Then, selective constraints specific to given proteins are approximated as a linear function of those estimated from the empirical substitution matrices.

Results

Akaike information criterion (AIC) values indicate that a model allo

SUBMITTER: Miyazawa S 

PROVIDER: S-EPMC3060808 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature