essaMEM: finding maximal exact matches using enhanced sparse suffix arrays.
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.
Department of Applied Mathematics and Computer Science and Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent B-9000, Belgium. Michael.Vyverman@UGent.be
Michaël
M
Vyverman
Bernard
B
De Baets
Veerle
V
Fack
Peter
P
Dawyndt
D000465:Algorithms; D000818:Animals; D004330:Drosophila / Q000235:genetics; D016678:Genome; D017421:Sequence Analysis / Q000379:methods*; D012984:Software