Substitution matrix

This article is about the use of a stochastic matrix to model evolution in bioinformatics. For the economics concept also called the Slutsky matrix, see Slutsky equation.

In bioinformatics and evolutionary biology, a substitution matrix describes the frequency at which a character in a nucleotide sequence or a protein sequence changes to other character states over evolutionary time. The information is often in the form of log odds of finding two specific character states aligned and depends on the assumed number of evolutionary changes or sequence dissimilarity between compared sequences. It is an application of a stochastic matrix. Substitution matrices are usually seen in the context of amino acid or DNA sequence alignments, where they are used to calculate similarity scores between the aligned sequences.[1]

  1. ^ Zvelebil, Marketa J. (2008). Understanding bioinformatics. New York: Garland Science. pp. 117–127, 747. ISBN 978-0-8153-4024-9.