Cite as: Cold Spring Harb. Protoc.; 2008; doi:10.1101/pdb.ip58

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A Test of the Markov Model of Evolution in Proteins

David W. Mount

Adapted from "Alignment of Pairs of Sequences," Chapter 3, in Bioinformatics: Sequence and Genome Analysis, 2nd edition, by David W. Mount. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 2004.


INTRODUCTION

The percent accepted mutation (PAM) scoring matrix is based on the Dayhoff model of protein evolution, which is a Markov process. In the Markov model of amino acid change, the probability of mutation at each site is independent of the previous history of mutations. Use of this model makes it possible to extrapolate amino acid substitutions observed over a relatively short period of evolutionary time to longer periods of evolutionary time. One criticism of the PAM scoring matrix is that the frequency of amino acid changes that require two nucleotide changes is higher than would be expected by chance. This article describes a test of the Markov model of protein evolution, which shows that the model can be valid if certain changes are made in the way that PAM matrices are calculated.


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