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==Other biological uses==
Sequenced RNA, such as [[expressed sequence tags]] and full-length mRNAs, can be aligned to a sequenced genome to find where there are genes and get information about [[alternative splicing]]<ref>{{cite book |author1=Kim N |author2=Lee C |title=Bioinformatics |chapter=Bioinformatics Detection of Alternative Splicing |volume=452 |pages=179–97 |year=2008 |pmid=18566765 |doi=10.1007/978-1-60327-159-2_9 |series=Methods in Molecular Biology |isbn=978-1-58829-707-5}}</ref> and [[RNA editing]].<ref>{{cite journal |vauthors=Li JB, Levanon EY, Yoon JK, etal |title=Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing |journal=Science |volume=324 |issue=5931 |pages=1210–3 |date=May 2009 |pmid=19478186 |doi=10.1126/science.1170995|bibcode=2009Sci...324.1210L |s2cid=31148824 }}</ref> Sequence alignment is also a part of [[genome assembly]], where sequences are aligned to find overlap so that ''[[contig]]s'' (long stretches of sequence) can be formed.<ref>{{cite journal |vauthors=Blazewicz J, Bryja M, Figlerowicz M, etal |title=Whole genome assembly from 454 sequencing output via modified DNA graph concept |journal=Comput Biol Chem |volume=33 |issue=3 |pages=224–30 |date=June 2009 |pmid=19477687 |doi=10.1016/j.compbiolchem.2009.04.005}}</ref> Another use is [[single nucleotide polymorphism|SNP]] analysis, where sequences from different individuals are aligned to find single basepairs that are often different in a population.<ref>{{cite journal |author1=Duran C |author2=Appleby N |author3=Vardy M |author4=Imelfort M |author5=Edwards D |author6=Batley J |title=Single nucleotide polymorphism discovery in barley using autoSNPdb |journal=Plant Biotechnol. J. |volume=7 |issue=4 |pages=326–33 |date=May 2009 |pmid=19386041 |doi=10.1111/j.1467-7652.2009.00407.x |doi-access=free |bibcode=2009PBioJ...7..326D }}</ref>
==Non-biological uses==
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