Substitution matrix: Difference between revisions

Revision as of 13:47, 21 December 2023

Revision as of 07:00, 24 September 2024

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{{short description|Matrix representing the frequency of evolution of a protein or nucleotide sequence}}

{{about|the use of a stochastic matrix to model evolution in bioinformatics|the economics concept also called the Slutsky matrix|Slutsky equation}}

{{More footnotes|article|date=October 2009}}

In [[bioinformatics]] and [[evolutionary biology]], a '''substitution matrix''' describes the frequency at which a character in a [[Nucleic acid sequence|nucleotide sequence]] or a [[Protein primary structure|protein sequence]] changes to other character states over evolutionary[[evolution]]ary time. The information is often in the form of [[Logit|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 alignment]]s, where they are used to calculate similarity scores between the aligned sequences.<ref name="Zvelebil">{{cite book |last1=Zvelebil |first1=Marketa J. |title=Understanding bioinformatics |date=2008 |publisher=Garland Science |___location=New York |isbn=978-0-8153-4024-9 |pages=117–127, 747}}</ref>

== Background ==