SpEED: fast computation of sensitive spaced seeds

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Abstract

Summary: 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.

Availability: The source code of SpEED is freely available at www.csd.uwo.ca/~ilie/SpEED/

Contact:ilie@csd.uwo.ca

Supplementary information: Supplementary data are available at Bioinformatics online.

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