Menu
Home
People
Places
Arts
History
Plants & Animals
Science
Life & Culture
Technology
Reference.org
Multiple sequence alignment
open-in-new
<p>Multiple sequence alignment (MSA) is the process or the result of <a href="/facts/Sequence_alignment/p8GQfF7b">sequence alignment</a> of three or more <a href="/facts/Biological_sequence/VaN6MEYh">biological sequences</a>, generally <a href="/facts/Protein/Jxmagu3E">protein</a>, <a href="/facts/DNA/nB89Iauz">DNA</a>, or <a href="/facts/RNA/HxPeNfNj">RNA</a>. These alignments are used to infer <a href="/facts/Evolutionary/TuWap5IK">evolutionary</a> relationships via <a href="/facts/Phylogenetic/bw4rsovt">phylogenetic</a> analysis and can highlight <a href="/facts/Homology_(biology)/muctKlyT">homologous</a> features between sequences. Alignments highlight <a href="/facts/Mutation/Ee4NnWbY">mutation</a> events such as <a href="/facts/Point_mutations/q30PEGFd">point mutations</a> (single <a href="/facts/Amino_acid/WDxYwBny">amino acid</a> or <a href="/facts/Nucleotide/pQKEwlJI">nucleotide</a> changes), <a href="/facts/Insertion_mutation/LC827MUs">insertion mutations</a> and <a href="/facts/Deletion_mutation/6TRPY0ys">deletion mutations</a>, and alignments are used to assess sequence <a href="/facts/Conservation_(genetics)/YAxy2Xa2">conservation</a> and infer the presence and activity of <a href="/facts/Protein_domain/oUpFcSsl">protein domains</a>, <a href="/facts/Tertiary_structure/VaN6MEYh">tertiary structures</a>, <a href="/facts/Secondary_structure/VaN6MEYh">secondary structures</a>, and individual amino acids or nucleotides. </p><p>Multiple sequence alignments require more sophisticated methodologies than <a href="/facts/Sequence_alignment/p8GQfF7b">pairwise alignments</a>, as they are more <a href="/facts/Computational_complexity_theory/etHuVF3U">computationally complex</a>. Most multiple sequence alignment programs use <a href="/facts/Heuristic/BcBEkv9c">heuristic</a> methods rather than <a href="/facts/Global_optimization/nksWlDqU">global optimization</a> because identifying the optimal alignment between more than a few sequences of moderate length is prohibitively computationally expensive. However, heuristic methods generally cannot guarantee high-quality solutions and have been shown to fail to yield near-optimal solutions on benchmark test cases. </p>