Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition
نویسندگان
چکیده
منابع مشابه
Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition
The measurement of synonymous and non-synonymous substitution rates (dS and dN) is useful for assessing selection operating on protein sequences or for investigating mutational processes affecting genomes. In particular, the ratio dNdS is expected to be a good proxy for ω, the ratio of fixation robabilities of non-synonymous mutations relative to that of neutral mutations. Standard methods for ...
متن کاملEstimating synonymous and nonsynonymous substitution rates.
Partitioning the total substitution rate into synnonymous and nonsynonymous components is a key aspect of many analyses in molecular evolution. Numerous methods exist for estimating these rates. However, until recently none of the estimation procedures were based on a sound statistical footing. In this paper, the evolutionary model of Muse and Gaut (1994) is used as the basis for two sets of pa...
متن کاملEstimating synonymous and nonsynonymous substitution rates under realistic evolutionary models.
Approximate methods for estimating the numbers of synonymous and nonsynonymous substitutions between two DNA sequences involve three steps: counting of synonymous and nonsynonymous sites in the two sequences, counting of synonymous and nonsynonymous differences between the two sequences, and correcting for multiple substitutions at the same site. We examine complexities involved in those steps ...
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We compared the rates of synonymous (silent) substitution among various genes in a number of species of Drosophila. First, we found that even for a particular gene, the rate of synonymous substitution varied considerably with Drosophila lineages. Second, we showed a large variation in synonymous substitution rates among nuclear genes in Drosophila. These rates of synonymous substitution were co...
متن کاملNonlinear Dynamics of Nonsynonymous (dN) and Synonymous (dS) Substitution Rates Affects Inference of Selection
Selection modulates gene sequence evolution in different ways by constraining potential changes of amino acid sequences (purifying selection) or by favoring new and adaptive genetic variants (positive selection). The number of nonsynonymous differences in a pair of protein-coding sequences can be used to quantify the mode and strength of selection. To control for regional variation in substitut...
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ژورنال
عنوان ژورنال: Molecular Biology and Evolution
سال: 2017
ISSN: 0737-4038,1537-1719
DOI: 10.1093/molbev/msx308