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


BACKGROUND
Source code is freely available at (http://www.cs.wisc.edu/~jignesh/probematch/).
Department of EECS, The University of Michigan, Ann Arbor, MI, USA.
You Jung
YJ
Kim
Nikhil
N
Teletia
Victor
V
Ruotti
Christopher A
CA
Maher
Arul M
AM
Chinnaiyan
Ron
R
Stewart
James A
JA
Thomson
Jignesh M
JM
Patel
D030541:Databases, Genetic; D016678:Genome / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D009841:Oligonucleotides / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
D009841:Oligonucleotides