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…

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.

Provides a practical solution for finding MEMs between arbitrarily large…

Provides a practical solution for finding MEMs between arbitrarily large genomes. E-MEM uses much less memory than the currently available programs. This algorithm uses much less space and is highly…

An algorithm for finding MEMs. The algorithm leverages a sparse suffix array…

An algorithm for finding MEMs. The algorithm leverages a sparse suffix array (SA), a text index that stores every K-th position of the text. In contrast to a full text index that stores every…

A tool for finding maximal exact matches that can be used in genome comparison…

A tool for finding maximal exact matches that can be used in genome comparison and read mapping. essaMEM enhances an existing sparse suffix array implementation with a sparse child array. Tests…

A tool used to efficiently retrieve maximal exact matches (MEMs) between a…

A tool used to efficiently retrieve maximal exact matches (MEMs) between a reference sequence and one or more query sequences. slaMEM relies on an FM-Index together with a new data structure called…