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{{More citations needed|date=March 2009}}
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><ref>{{Cite book |last=Gagniuc |first=Paul A. |url=https://www.worldcat.org/oclc/1240827446 |title=Algorithms in bioinformatics: theory and implementation |date=2021 |publisher=John Wiley & Sons |year=2021 |isbn=978-1-119-69800-5 |edition=1st |___location=Hoboken, NJ |pages=1-528 |language=English |oclc=1240827446}}</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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