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Analysis of amino acid substitution during divergent evolution: the 400 by 400 dipeptide substitution matrix.

Abstract：

:Most formal methods for analyzing the divergent evolution of protein sequences assume a Markov model where position i in a polypeptide chain undergoes amino acid substitution independently from position i + 1. The large number of aligned homologous sequence pairs available from the exhaustive matching of the protein sequence database makes it possible to examine this assumption empirically. We have constructed a 400 by 400 matrix that reports empirical probabilities for the interconversion of all pairs of dipeptides in proteins undergoing divergent evolution. Comparison of these probabilities with those expected if substitution at adjacent positions in a protein sequence were independent reveals interesting patterns that arise through the breakdown of this assumption. Several of these are useful in extracting conformational information from patterns of conservation and variation in homologous protein sequences.

journal_name

Biochem Biophys Res Commun

journal_title

Biochemical and biophysical research communications

authors

Gonnet GH,Cohen MA,Benner SA

doi

10.1006/bbrc.1994.1255

subject

Has Abstract

pub_date

1994-03-15 00:00:00

pages

489-96

issue

2

eissn

0006-291X

issn

1090-2104

pii

S0006-291X(84)71255-1

journal_volume

199

pub_type

杂志文章

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