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Maximal exact matches (MEMs) are exact matches between two strings that cannot be extended in either direction towards the beginning or end of two strings without allowing for a mismatch. Algorithms for computing MEMs between sequences appear in two contexts where high-throughput sequencing will vastly increase the volume of sequence data: (i) seeding alignments of high-throughput sequencing reads for genome assembly and (ii) designating anchor points for genome–genome comparisons when the two genomes are relatively similar.
(Khan et al., 2009) A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays. Bioinformatics.