PATTERNHUNTER is a highly sensitive and efficient program for finding homologies within one, or between two DNA sequences. On very long sequences it runs faster than MegaBlast while being more sensitive than Blastn (at its default settings).

This track was produced by having PATTERNHUNTER index each human chromosome 22 and processing all mouse reads in turn, looking for double hits of weight 11 (using size 18 words with 7 don't cares in the pattern 111010011001010111) to extend from and form gapped alignments.

More information about PATTERNHUNTER is available at Bioinformatics Solutions Inc. See also Ma B, Tromp J, Li M. PatternHunter: Faster and more sensitive homology search. Bioinformatics. 2002 Mar;18(3):440-5.