Pitfalls of the most commonly used models of context dependent substitution.

ABSTRACT:

Background

Neighboring nucleotides exert a striking influence on mutation, with the hypermutability of CpG dinucleotides in many genomes being an exemplar. Among the approaches employed to measure the relative importance of sequence neighbors on molecular evolution have been continuous-time Markov process models for substitutions that treat sequences as a series of independent tuples. The most widely used examples are the codon substitution models. We evaluated the suitability of derivatives of the nucleotide frequency weighted (hereafter NF) and tuple frequency weighted (hereafter TF) models for measuring sequence context dependent substitution. Critical properties we address are their relationships to an independent nucleotide process and the robustness of parameter estimation to

SUBMITTER: Lindsay H 

PROVIDER: S-EPMC2628887 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature