Overlap digraph: An effective model for finding good spaced seeds for biological sequence local alignment

Spaced seeds technology, which was proposed by PatternHunter, has been proven to be more sensitive and faster than continuous seeds, and it is now widely used for bio-sequence local alignments. However, finding optimal spaced seeds is an NP-hard problem. A seed digraph model is proposed to find good spaced seeds, which are very close to optimal, in a very different but effective way. Using this different approach, some good long spaced seeds which cannot be calculated by normal optimal sensitivity formulas due to their exponential complexity can be found.