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In [[bioinformatics]], a '''sequence alignment''' is a way of arranging the sequences of [[DNA]], [[RNA]], or protein to identify regions of similarity that may be a consequence of functional, [[structural biology|structural]], or [[evolution]]ary relationships between the sequences.<ref name=mount>{{cite book| author=Mount DM.| year=2004 | title=Bioinformatics: Sequence and Genome Analysis |edition=2nd | publisher= Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY. |isbn=978-0-87969-608-5}}</ref> Aligned sequences of [[nucleotide]] or [[amino acid]] residues are typically represented as rows within a [[matrix (mathematics)|matrix]]. Gaps are inserted between the [[Residue (chemistry)|residues]] so that identical or similar characters are aligned in successive columns.
Sequence alignments are also used for non-biological sequences, such as calculating the [[Edit distance|distance cost]] between strings in a [[natural language]] or in financial data.
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[[File:Histone Alignment.png|thumb|595px|A sequence alignment, produced by [[ClustalO]], of mammalian [[histone]] proteins. <br />
Sequences are the [[Amino acid#Table of standard amino acid abbreviations and properties|amino acids]] for residues 120-180 of the proteins. Residues that are conserved across all sequences are highlighted in grey. Below the protein sequences is a key denoting [[conserved sequence]] (*), [[conservative mutation]]s (:), semi-conservative mutations (.), and [[segregating site|non-conservative mutations]] ( ).<ref>{{cite web|url=http://www.ebi.ac.uk/Tools/msa/clustalw2/help/faq.html#23|website=Clustal|title=Clustal FAQ #Symbols|access-date=8 December 2014|archive-url=https://web.archive.org/web/20161024045656/http://www.ebi.ac.uk/Tools/msa/clustalw2/help/faq.html#23|archive-date=24 October 2016|url-status=dead}}</ref>]]
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