Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites

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Abstract

A general model for estimating the number of amino acid substitutions per site (d) from the fraction of identical residues between two sequences (q) is proposed. The well-known Poisson-correction formula q = e(-d) corresponds to a site-independent and amino-acid-independent substitution rate. Equation q = (1 - e(-2d)/2d, derived for the case of substitution rates that are site- independent, but vary among amino acids, approximates closely the empirical method, suggested by Dayhoff et al. (1978). Equation q = 1/(1 + d) describes the case of substitution rates that are amino acid-independent but vary among sites. Lastly, equation q = [1n(1 + 2d)1/2d accounts for the general case where substitution rates can differ for both amino acids and sites.

Original languageEnglish (US)
Pages (from-to)675-679
Number of pages5
JournalJournal of Molecular Evolution
Volume41
Issue number5
StatePublished - 1995

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amino acid substitution
Amino Acid Substitution
substitution
Substitution reactions
amino acid
Amino Acids
amino acids
rate
methodology

Keywords

  • Amino acid substitutions
  • Dayhoff et al.'s distance
  • Evolutionary distance
  • Gamma distance
  • PAM scale

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)
  • Genetics(clinical)
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Agricultural and Biological Sciences(all)
  • Agricultural and Biological Sciences (miscellaneous)

Cite this

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abstract = "A general model for estimating the number of amino acid substitutions per site (d) from the fraction of identical residues between two sequences (q) is proposed. The well-known Poisson-correction formula q = e(-d) corresponds to a site-independent and amino-acid-independent substitution rate. Equation q = (1 - e(-2d)/2d, derived for the case of substitution rates that are site- independent, but vary among amino acids, approximates closely the empirical method, suggested by Dayhoff et al. (1978). Equation q = 1/(1 + d) describes the case of substitution rates that are amino acid-independent but vary among sites. Lastly, equation q = [1n(1 + 2d)1/2d accounts for the general case where substitution rates can differ for both amino acids and sites.",
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PY - 1995

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AB - A general model for estimating the number of amino acid substitutions per site (d) from the fraction of identical residues between two sequences (q) is proposed. The well-known Poisson-correction formula q = e(-d) corresponds to a site-independent and amino-acid-independent substitution rate. Equation q = (1 - e(-2d)/2d, derived for the case of substitution rates that are site- independent, but vary among amino acids, approximates closely the empirical method, suggested by Dayhoff et al. (1978). Equation q = 1/(1 + d) describes the case of substitution rates that are amino acid-independent but vary among sites. Lastly, equation q = [1n(1 + 2d)1/2d accounts for the general case where substitution rates can differ for both amino acids and sites.

KW - Amino acid substitutions

KW - Dayhoff et al.'s distance

KW - Evolutionary distance

KW - Gamma distance

KW - PAM scale

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