Journal Article

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

You Jung Kim, Nikhil Teletia, Victor Ruotti, Christopher A. Maher, Arul M. Chinnaiyan, Ron Stewart, James A. Thomson and Jignesh M. Patel

in Bioinformatics

Volume 25, issue 11, pages 1424-1425
Published in print June 2009 | ISSN: 1367-4803
Published online April 2009 | e-ISSN: 1460-2059 | DOI:
ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches

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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∼jignesh/probematch/


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1446 words. 

Subjects: Bioinformatics and Computational Biology

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