ProbeMatch is a sequence alignment program designed for matching a large set of oligonucleotide sequences against a genome database using gapped alignments. Unlike existing tools such as ELAND and MAQ which only perform ungapped alignments allowing at most 2-3 mismatches, ProbeMatch generates both ungapped and gapped alignments allowing up to 3 errors including insertion, deletion, and mismatch.
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Bioinformatics. 2009 Jun 1;25(11):1424-5. doi: 10.1093/bioinformatics/btp178. Epub 2009 Apr 7.
ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches.
Kim YJ1, Teletia N, Ruotti V, Maher CA, Chinnaiyan AM, Stewart R, Thomson JA, Patel JM.