SpEED: fast computation of sensitive spaced seeds
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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: email@example.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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