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Bioinformatics Advance Access published online on April 7, 2009
Bioinformatics, 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 : A tool for aligning oligonucleotide sequences

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

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

*To whom correspondence should be addressed. Prof. Jignesh Patel, E-mail: jignesh{at}eecs.umich.edu


  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 2 mismatches, ProbeMatch generates both ungapped and gapped alignments allowing up to 3 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 sequencesto 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 hour.

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

Contact: teletia{at}cs.wisc.edu

Associate Editor: Prof. Dmitrij Frishman

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

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