Correlation Between the Substitution Rate and Rate Variation Among Sites in Protein Evolution
نویسندگان
چکیده
منابع مشابه
Correlation between the substitution rate and rate variation among sites in protein evolution.
It is well known that the rate of amino acid substitution varies among different proteins and among different sites of a protein. It is, however, unclear whether the extent of rate variation among sites of a protein and the mean substitution rate of the protein are correlated. We used two approaches to analyze orthologous protein sequences of 51 nuclear genes of vertebrates and 13 mitochondrial...
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Substitution-rate variation among sites and the estimation of transition bias.
Substitution-rate variation among sites and differences in the probabilities of change among the four nucleotides are conflated in DNA sequence comparisons. When variation in rate exists among sites but is ignored, biases in the rates of change among nucleotides are underestimated. This paper provides a quantification of this effect when the observed proportions of transitions, P, and transvers...
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Mitochondrial D-loop hypervariable region I (HVI) sequences are widely used in human molecular evolutionary studies, and therefore accurate assessment of rate heterogeneity among sites is essential. We used the maximum-likelihood method to estimate the gamma shape parameter alpha for variable substitution rates among sites for HVI from humans and chimpanzees to provide estimates for future stud...
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When the rate variation among sites is described by a gamma distribution, an important problem is how to estimate the shape parameter 01, which is an index of the degree of among-site rate variation. The parsimony-based methods for estimating (Y are simple but biased, i.e., (Y tends to be overestimated. On the other hand, the likelihood-based methods are asymptotically unbiased but take a huge ...
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ژورنال
عنوان ژورنال: Genetics
سال: 1998
ISSN: 1943-2631
DOI: 10.1093/genetics/149.3.1615