Efficient q-Gram Filters for Finding All ε-Matches over a Given Length

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Abstract
Fast and exact comparison of large genomic sequences remains a challenging task in biosequence analysis. We consider the problem of finding all ε-matches between two sequences, i.e., all local alignments over a given length with an error rate of at most ε. 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.