essaMEM: finding maximal exact matches using enhanced sparse suffix arrays | Zendy

Michaël Vyverman | Zendy; Bernard De Baets | Zendy; Veerle Fack | Zendy; Peter Dawyndt | Zendy

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essaMEM: finding maximal exact matches using enhanced sparse suffix arrays

Author(s) -

Michaël Vyverman,

Bernard De Baets,

Veerle Fack,

Peter Dawyndt

Publication year - 2013

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btt042

Subject(s) - compressed suffix array , suffix , suffix array , computer science , memory footprint , algorithm , sparse array , footprint , suffix tree , data structure , theoretical computer science , programming language , paleontology , linguistics , philosophy , biology

We have developed essaMEM, 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 indicate that the enhanced algorithm for finding maximal exact matches is much faster, while maintaining the same memory footprint. In this way, sparse suffix arrays remain competitive with the more complex compressed suffix arrays.

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