PatternHunter II: Highly Sensitive and Fast Homology Search

Ming Li[1] (mli@uwaterloo.ca)
Bin Ma[2] (bma@csd.uwo.ca)
Derek Kisman[3] (dkisman@BioinformaticsSolutions.com)
John Tromp[4] (tromp@cwi.nl)

[1]Dept. Computer Science, Univ. of Waterloo, Waterloo, ON, Canada N2L 3G1.
[2]Dept. Computer Science, Univ. of Western Ontario, London, ON, Canada N6A 5B7.
[3]Bioinformatics Solutions Inc., 2B-145 Columbia W., Waterloo, ON, Canada N2L 3L2.
[4]CWI, P.O. Box 94079, 1090 GB Amsterdam, The Netherlands.

Abstract

Extending the single optimized spaced seed of PatternHunter \cite{ph} 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.

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