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Faster Bit-Parallel Approximate String Matching

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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 present a new bit-parallel technique for approximate string matching. We build on two previous techniques. The first one [Myers, J. of the ACM, 1999], searches for a pattern of length m in a text of length n permitting k differences in O(mn/w) time, where w is the width of the computer word. The second one [Navarro and Raffinot, ACM JEA, 2000], extends a sublinear-time exact algorithm to approximate searching. The latter technique makes use of an O(kmn/w) time algorithm [Wu and Manber, Comm. ACM, 1992] for its internal workings. This algorithm is slow but flexible enough to support all the required operations. In this paper we show that the faster algorithm of Myers can be adapted to support all those operations. This involves extending it to compute edit distance, to search for any pattern suffix, and to detect in advance the impossibility of a later match. The result is an algorithm that performs better than the original version of Navarro and Raffinot and that is the fastest for several combinations of m, k and alphabet sizes that are useful, for example, in natural language searching and computational biology.

Supported by the Academy of Finland and Tampere Graduate School in Information Science and Engineering.

Partially supported by Fondecyt Project 1-020831.

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Author information

Authors and Affiliations

  1. Dept. of Computer and Information Sciences, University of Tampere, Finland

    Heikki Hyyrö

  2. Dept. of Computer Science, University of Chile, Chile

    Gonzalo Navarro

Authors
  1. Heikki Hyyrö
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  2. Gonzalo Navarro
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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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Hyyrö, H., Navarro, G. (2002). Faster Bit-Parallel Approximate String Matching. 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_18

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  • DOI: https://doi.org/10.1007/3-540-45452-7_18

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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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