Efficient q-gram filters for finding all ε-matches over a given length

Authors:
Kim R. Rasmussen;Jens Stoye;Eugene W. Myers
Affiliations:
International NRW Graduate School in Bioinformatics and Genome Research, Center of Biotechnology, Universität Bielefeld, Bielefeld, Germany;Technische Fakultät, Universität Bielefeld, Bielefeld, Germany;Div. of Computer Science, UC Berkeley, Berkeley, CA
Venue:
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
Year:
2005

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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.