### 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 language | English (US) |
---|---|

Pages (from-to) | 675-679 |

Number of pages | 5 |

Journal | Journal of Molecular Evolution |

Volume | 41 |

Issue number | 5 |

State | Published - 1995 |

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### 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

**Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites.** / Grishin, N. V.

Research output: Contribution to journal › Article

*Journal of Molecular Evolution*, vol. 41, no. 5, pp. 675-679.

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TY - JOUR

T1 - Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites

AU - Grishin, N. V.

PY - 1995

Y1 - 1995

N2 - 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.

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

UR - http://www.scopus.com/inward/record.url?scp=0028818963&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0028818963&partnerID=8YFLogxK

M3 - Article

VL - 41

SP - 675

EP - 679

JO - Journal of Molecular Evolution

JF - Journal of Molecular Evolution

SN - 0022-2844

IS - 5

ER -