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One-Gapped q-Gram Filters for Levenshtein Distance

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Combinatorial Pattern Matching (CPM 2002)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2373))

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Abstract

We have recently shown that q- gram filters based on gapped q-grams instead of the usual contiguous q-grams can provide orders of magnitude faster and/or more efficient filtering for the Hamming distance. In this paper, we extend the results for the Levenshtein distance, which is more problematic for gapped q-grams because an insertion or deletion in a gap affects a q-gram while a replacement does not. To keep this effect under control, we concentrate on gapped q-grams with just one gap. We demostrate with experiments that the resulting filters provide a significant improvement over the contiguous q-gram filters. We also develop new techniques for dealing with complex q-gram filters.

Supported by the DFG ‘Initiative Bioinformatik’ grant BIZ 4/1-1.

Partially supported by the Future and Emerging Technologies programme of the EU under contract number IST-1999-14186 (ALCOM-FT).

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Author information

Authors and Affiliations

  1. Center for Bioinformatics, Saarland University, Postfach 151150, 66041, Saarbrücken, Germany

    Stefan Burkhardt

  2. Max-Planck-Institut für Informatik, Stuhlsatzenhausweg 85, 66123, Saarbrücken, Germany

    Juha Kärkkäinen

Authors
  1. Stefan Burkhardt
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  2. Juha Kärkkäinen
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Editor information

Editors and Affiliations

  1. Department of Electrial Engineering and Computer Science, University of Padova, Via Gradenigo 6/A, 35131, Padova, Italy

    Alberto Apostolico

  2. Department of Informatics, Kyushu University, Fukuoka 812-8581, Japan

    Masayuki Takeda

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© 2002 Springer-Verlag Berlin Heidelberg

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Burkhardt, S., Kärkkäinen, J. (2002). One-Gapped q-Gram Filters for Levenshtein Distance. In: Apostolico, A., Takeda, M. (eds) Combinatorial Pattern Matching. CPM 2002. Lecture Notes in Computer Science, vol 2373. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45452-7_19

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  • DOI: https://doi.org/10.1007/3-540-45452-7_19

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-43862-5

  • Online ISBN: 978-3-540-45452-6

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