Journal
JOURNAL OF COMPUTATIONAL BIOLOGY
Volume 13, Issue 2, Pages 296-308Publisher
MARY ANN LIEBERT, INC
DOI: 10.1089/cmb.2006.13.296
Keywords
q-grams; filter; local alignment searching; sequence assembly; EST clustering
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Fast and exact comparison of large genomic sequences remains a challenging task in biosequence analysis. We consider the problem of finding all epsilon-matches between two sequences, i.e., all local alignments over a given length with an error rate of at most epsilon. We study this problem theoretically, giving an efficient q-gram filter for solving it. Two applications of the filter are also discussed, in particular genomic sequence assembly and BLAST-like sequence comparison. Our results show that the method is 25 times faster than BLAST, while not being heuristic.
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