MUM

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.