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Bioinformatics Advance Access originally published online on April 7, 2009
Bioinformatics 2009 25(11):1424-1425; doi:10.1093/bioinformatics/btp178
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches

You Jung Kim 1, Nikhil Teletia 2, Victor Ruotti 3, Christopher A. Maher 4, Arul M. Chinnaiyan 4, Ron Stewart 3, James A. Thomson 3,5 and Jignesh M. Patel 2,*

1Department of EECS, The University of Michigan, Ann Arbor, MI, 2Computer Science Department, The University of Wisconsin, 3Morgridge Institute for Research, Madison, WI, 4Department of Pathology, The University of Michigan, Ann Arbor, MI and 5University of Wisconsin School of Medicine and Public Health, Madison, WI, USA

*To whom correspondence should be addressed.


  Abstract

Summary: We have developed a tool, called ProbeMatch, for matching a large set of oligonucleotide sequences against a genome database using gapped alignments. Unlike most of the existing tools such as ELAND which only perform ungapped alignments allowing at most two mismatches, ProbeMatch generates both ungapped and gapped alignments allowing up to three errors including insertion, deletion and mismatch. To speedup sequence alignment, ProbeMatch uses gapped q-grams and q-grams of various patterns to identify target hits to a query sequence. This approach results in fewer initial sequences to examine with no loss in sensitivity. ProbeMatch has been used to align 169 095 Illumina GAII reads against the human genome, which could not be mapped by ELAND, and found alignments for 28 625 reads of the 169 095 reads in less than 3 h.

Availability: Source code is freely available at http://www.cs.wisc.edu/~jignesh/probematch/

Contact: jignesh{at}cs.wisc.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Dmitrij Frishman

Received on November 29, 2008; revised on March 7, 2009; accepted on March 25, 2009

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