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A number of terms have arisen in the field of comparative genomics. This page explains some typical terms associated with local matches. | |||
==MEM== | ==MEM== | ||
A ''maximal exact match'' is a sequence that matches exactly that cannot be extended in the 5' or the 3' direction (or N/C direction for proteins) without incurring a mismatch. Typically a filter is used to ensure MEMs are of length '''k''' or more (so-called '''k-mers'''.) | A ''maximal exact match'' is a sequence that matches exactly that cannot be extended in the 5' or the 3' direction (or N/C direction for proteins) without incurring a mismatch. Typically a filter is used to ensure MEMs are of length '''k''' or more (so-called '''k-mers'''.) | ||
A ''multi-MEM'' takes the idea of MEMs and applies it to multiple-alignments. Instead of a pair of sequences, multiMEMs contain 3 or more sequences. | |||
==MUM== | |||
A ''maximal unique match'' is a sequence of at least '''k''' residues that exists exactly once in the query and subject sequences. This is a way to overcome repetitive elements when aligning two sequences. The same idea of a multiMEM can be applied to the MUM, creating a multiMUM, a unique sequence that exists once in '''each''' aligned genome. | |||
Latest revision as of 19:53, 24 November 2009
A number of terms have arisen in the field of comparative genomics. This page explains some typical terms associated with local matches.
MEM
A maximal exact match is a sequence that matches exactly that cannot be extended in the 5' or the 3' direction (or N/C direction for proteins) without incurring a mismatch. Typically a filter is used to ensure MEMs are of length k or more (so-called k-mers.)
A multi-MEM takes the idea of MEMs and applies it to multiple-alignments. Instead of a pair of sequences, multiMEMs contain 3 or more sequences.
MUM
A maximal unique match is a sequence of at least k residues that exists exactly once in the query and subject sequences. This is a way to overcome repetitive elements when aligning two sequences. The same idea of a multiMEM can be applied to the MUM, creating a multiMUM, a unique sequence that exists once in each aligned genome.