SpEED: fast computation of sensitive spaced seeds

Abstract

Multiple spaced seeds represent the current state-of-the-art for similarity search in bioinformatics, with applications in various areas such as sequence alignment, read mapping, oligonucleotide design, etc. We present SpEED, a software program that computes highly sensitive multiple spaced seeds. SpEED can be several orders of magnitude faster and computes better seeds than the existing leading software programs. The source code of SpEED is freely available at www.csd.uwo.ca/~ilie/SpEED/ CONTACT: ilie@csd.uwo.ca Supplementary data are available at Bioinformatics online.