SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage.

ABSTRACT: Gene sequences are the target of evolution operating at different levels, including the nucleotide, codon, and amino acid levels. Disentangling the impact of those different levels on gene sequences requires developing a probabilistic model with three layers. Here we present SENCA (site evolution of nucleotides, codons, and amino acids), a codon substitution model that separately describes 1) nucleotide processes which apply on all sites of a sequence such as the mutational bias, 2) preferences between synonymous codons, and 3) preferences among amino acids. We argue that most synonymous substitutions are not neutral and that SENCA provides more accurate estimates of selection compared with more classical codon sequence models. We study the forces that drive the genomic content evolution,

SUBMITTER: Pouyet F 

PROVIDER: S-EPMC5010899 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature