SpEED: fast computation of sensitive spaced seeds

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.