Estimation of DNA sequence context-dependent mutation rates using primate genomic sequences.

摘要: It is understood that DNA and amino acid substitution rates are highly sequence context-dependent, e.g., C→T substitutions in vertebrates may occur much more frequently at CpG sites cysteine depend on support of the context for participation a disulfide bond. Furthermore, many applications rely quantitative models nucleotide or substitution, including phylogenetic inference identification positions involved functional specificity. We describe quantification dependence using baboon, chimpanzee, human genomic data generated by NISC Comparative Sequencing Program. Relative mutation reported 96 classes mutations form 5′αβγ3′ → 5′αδγ3′, where α, β, γ, δ nucleotides β ≠ δ, based maximum likelihood calculations. Our results confirm enhanced compared with other transitions, relatively independent identity preceding nucleotide. While, as expected, transitions generally than transversions, we find most frequent transversions involve C (CpG transversions) their rate comparable to non-CpG sites. A four-class model context-dependent evolution primate sequences, > ≈ captures qualitative features spectrum. despite similarity among different regions, there statistically significant differences.