منابع مشابه
A Generalized Mechanistic Codon Model
Models of codon evolution have attracted particular interest because of their unique capabilities to detect selection forces and their high fit when applied to sequence evolution. We described here a novel approach for modeling codon evolution, which is based on Kronecker product of matrices. The 61 × 61 codon substitution rate matrix is created using Kronecker product of three 4 × 4 nucleotide...
متن کاملA combined empirical and mechanistic codon model.
The evolutionary selection forces acting on a protein are commonly inferred using evolutionary codon models by contrasting the rate of synonymous to nonsynonymous substitutions. Most widely used models are based on theoretical assumptions and ignore the empirical observation that distinct amino acids differ in their replacement rates. In this paper, we develop a general method that allows assim...
متن کاملSelective Constraints on Amino Acids Estimated by a Mechanistic Codon Substitution Model with Multiple Nucleotide Changes
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 ov...
متن کاملAdvantages of a Mechanistic Codon Substitution Model for Evolutionary Analysis of Protein-Coding Sequences
BACKGROUND A mechanistic codon substitution model, in which each codon substitution rate is proportional to the product of a codon mutation rate and the average fixation probability depending on the type of amino acid replacement, has advantages over nucleotide, amino acid, and empirical codon substitution models in evolutionary analysis of protein-coding sequences. It can approximate a wide ra...
متن کاملA mechanistic model of photoinhibition
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ژورنال
عنوان ژورنال: Molecular Biology and Evolution
سال: 2014
ISSN: 1537-1719,0737-4038
DOI: 10.1093/molbev/msu196