Editing Sequence alignment (section)

===Maximal unique match===
One way of quantifying the utility of a given pairwise alignment is the '[[maximal unique match]]' (MUM), or the longest subsequence that occurs in both query sequences. Longer MUM sequences typically reflect closer relatedness.<ref name="Alignment of whole genomes">{{cite journal |last1=Delcher |first1=A. L. |last2=Kasif |first2=S. |last3=Fleishmann |first3=R.D. |last4=Peterson |first4=J. |last5=White |first5=O. |last6=Salzberg |first6=S.L. |title=Alignment of whole genomes |journal=Nucleic Acids Research |date=1999 |volume=27 |issue=11 |pages=2369–2376 |doi=10.1093/nar/30.11.2478 |pmid=10325427|pmc=148804 |doi-access=free }}</ref> in the [[multiple sequence alignment]] of [[genomes]] in [[computational biology]].  Identification of MUMs and other potential anchors, is the first step in larger alignment systems such as [[MUMmer]]. Anchors are the areas between two genomes where they are highly similar.  To understand what a MUM is we can break down each word in the acronym.  Match implies that the substring occurs in both sequences to be aligned.  Unique means that the substring occurs only once in each sequence.  Finally, maximal states that the substring is not part of another larger string that fulfills both prior requirements.  The idea behind this, is that long sequences that match exactly and occur only once in each genome are almost certainly part of the global alignment.

More precisely:

<blockquote>"Given two genomes A and B, Maximal Unique Match (MUM) substring is a common substring of A and B of length longer than a specified minimum length d (by default d= 20) such that
* it is maximal, that is, it cannot be extended on either end without incurring a mismatch; and
* it is unique in both sequences"<ref name="Algorithms in Bioinformatics">{{cite book |last1=Wing-Kin |first1=Sung |title=Algorithms in Bioinformatics: A Practical Introduction |date=2010 |publisher=Chapman & Hall/CRC Press |location=Boca Raton |isbn=978-1420070330 |edition=First}}</ref></blockquote>