PatternHunter II: highly sensitive and fast homology search.
Ming Li, Bin Ma, Derek Kisman, John Tromp · PubMed · 2003
Extending the single optimized spaced seed of PatternHunter to multiple ones, PatternHunter II simultaneously remedies the lack of sensitivity of Blastn and the lack of speed of Smith-Waterman, for homology search. At Blastn speed, PatternHunter II approaches Smith-Waterman sensitivity, bringing homology search technology back to a full circle.