Synonymous Nucleotide Divergence: What Is “Saturation”?
نویسندگان
چکیده
منابع مشابه
Synonymous nucleotide divergence: what is "saturation"?
The nucleotide divergence at synonymous third sites between two lineages will increase with time since the latest common ancestor, up to some saturation level. The "null-hypothesis divergence" is defined as the percentage of difference predicted at synonymous third sites, allowing for amino acid composition and codon bias, but assuming that codon bias is the same at all sites occupied by a give...
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MOTIVATION Functional divergence among proteins is often assumed to be strongly influenced by natural selection, as inferred from the ratio of non-synonymous nucleotide divergence (d(N)) to synonymous nucleotide divergence (d(S)). That is, the more a mutation changes protein function, the more likely it is to be either selected against or selectively favored, and because the d(N)/d(S) ratio is ...
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A mathematical model for codon substitution is presented, taking into account unequal mutation rates among different nucleotides and purifying selection. This model is constructed by using a 61 X 61 transition probability matrix for the 61 nonterminating codons. Under this model, a computer simulation is conducted to study the numbers of silent (synonymous) and amino acid-altering (nonsynonymou...
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ژورنال
عنوان ژورنال: Genetics
سال: 1996
ISSN: 1943-2631
DOI: 10.1093/genetics/142.3.1033