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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|
[[File:Histone Alignment.png|thumb|595px|A sequence alignment, produced by [[ClustalO]], of mammalian [[histone]] proteins. <br />
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