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Bioinformatics Advance Access originally published online on September 16, 2004
Bioinformatics 2005 21(4):542-544; doi:10.1093/bioinformatics/bti035
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Bioinformatics vol. 21 issue 4 © Oxford University Press 2005; all rights reserved.

tPatternHunter: gapped, fast and sensitive translated homology search

Derek Kisman 1, Ming Li 2, Bin Ma 3,* and Li Wang 3

1 Bioinformatics Solutions Inc. 145 Columbia St West, Waterloo, Ontario, Canada N2L 3L2
2 School of Computer Science, University of Waterloo Ontario, Canada N2L 3G1
3 Department of Computer Science, University of Western Ontario London, Ontario Canada N6A 5B7

*To whom correspondence should be addressed.

Summary: New ideas, spaced seeds and gapped alignment before 6-frame translation are implemented for translated homology search in tPatternHunter. The new software compares favorably with tBLASTx.

Availability: The software is free to academics at http://www.bioinformaticssolutions.com/downloads/ph-academic/

Contact: bma{at}csd.uwo.ca


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