Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection
نویسندگان
چکیده
منابع مشابه
Bayes empirical bayes inference of amino acid sites under positive selection.
Codon-based substitution models have been widely used to identify amino acid sites under positive selection in comparative analysis of protein-coding DNA sequences. The nonsynonymous-synonymous substitution rate ratio (d(N)/d(S), denoted omega) is used as a measure of selective pressure at the protein level, with omega > 1 indicating positive selection. Statistical distributions are used to mod...
متن کاملAccuracy and power of bayes prediction of amino acid sites under positive selection.
Bayes prediction quantifies uncertainty by assigning posterior probabilities. It was used to identify amino acids in a protein under recurrent diversifying selection indicated by higher nonsynonymous (d(N)) than synonymous (d(S)) substitution rates or by omega = d(N)/d(S) > 1. Parameters were estimated by maximum likelihood under a codon substitution model that assumed several classes of sites ...
متن کاملA counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection
MOTIVATION Statistical methods for comparing relative rates of synonymous and non-synonymous substitutions maintain a central role in detecting positive selection. To identify selection, researchers often estimate the ratio of these relative rates (dN/dS) at individual alignment sites. Fitting a codon substitution model that captures heterogeneity in dN/dS across sites provides a reliable way t...
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For the problem of variable selection for the normal linear model, fixed penalty selection criteria such as AIC, Cp, BIC and RIC correspond to the posterior modes of a hierarchical Bayes model for various fixed hyperparameter settings. Adaptive selection criteria obtained by empirical Bayes estimation of the hyperparameters have been shown by George and Foster [2000. Calibration and Empirical B...
متن کاملDetecting amino acid sites under positive selection and purifying selection.
An excess of nonsynonymous over synonymous substitution at individual amino acid sites is an important indicator that positive selection has affected the evolution of a protein between the extant sequences under study and their most recent common ancestor. Several methods exist to detect the presence, and sometimes location, of positively selected sites in alignments of protein-coding sequences...
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ژورنال
عنوان ژورنال: Molecular Biology and Evolution
سال: 2005
ISSN: 0737-4038,1537-1719
DOI: 10.1093/molbev/msi097