Fast and exact comparison of large genomic sequences remains a challenging task in biosequence analysis. We consider the problem of finding all e-matches between two sequences, i.e. all local alignments over a given length with an error rate of at most e. 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 is25 times faster than blast, while not being heuristic.
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