PatternHunter II: Highly Sensitive and Fast Homology Search

Abstract

Extending the single optimized spaced seed of PatternHunter [20] to multiple ones, Pattern-Hunter 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.