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The Max-Shift Algorithm for Approximate String Matching

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Algorithm Engineering (WAE 2001)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2141))

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Abstract

The approximate string matching problem is to find all locations which a pattern of length m matches a substring of a text of length n with at most k differences. The program agrep is a simple and practical bit-vector algorithm for this problem. In this paper we consider the following incremental version of the problem: given an appropriate encoding of a comparison between A and bB, can one compute the answer for A and B, and the answer for A and Bc with equal efficiency, where b and c are additional symbols? Here we present an elegant and very easy to implement bit-vector algorithm for answering these questions that requires only O(n⌈m/w⌉) time, where n is the length of A, m is the length of B and w is the number of bits in a machine word. We also present an O(nm⌈h/w⌉) algorithm for the fixed-length approximate string matching problem: given a text t, a pattern p and an integer h, compute the optimal alignment of all substrings of p of length h and a substring of t.

Partially supported by a Marie Curie fellowship and NATO, Wellcome and Royal Society grants.

Partially supported by the C.N.R.S. Program “Génomes”.

Partially supported by an ORS studentship and EPSRC Project GR/L92150.

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Author information

Authors and Affiliations

  1. Dept. of Computer Science, King’s College London, London, WC2R 2LS, England

    Costas S. Iliopoulos & Yoan J. Pinzon

  2. School of Computing, Curtin University of Technology, GPO Box 1987 U, WA

    Costas S. Iliopoulos & Yoan J. Pinzon

  3. ESA 6037: Dept. of Vegetal Physiology - ABISS, Université de Rouen, 76821 Mont Saint Aignan Cedex, France

    Laurent Mouchard

  4. School of Computing, Curtin University of Technology, GPO Box 1987 U, WA

    Laurent Mouchard

Authors
  1. Costas S. Iliopoulos
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  2. Laurent Mouchard
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  3. Yoan J. Pinzon
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Editor information

Editors and Affiliations

  1. Department of Computer Science, University of Aarhus, BRICS, 8000, Åarhus, Denmark

    Gerth Stølting Brodal

  2. Dipartimento di Ingegneria Elettrica, Universitá dell’Aquila, Poggio di Roio, 67040, L’Aquila, Italy

    Daniele Frigioni

  3. Dipartimento di Informatica e Sistemistica, Universitá di Roma “La Sapienza”, via Salaria 113, 00198, Roma, Italy

    Alberto Marchetti-Spaccamela

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© 2001 Springer-Verlag Berlin Heidelberg

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Iliopoulos, C.S., Mouchard, L., Pinzon, Y.J. (2001). The Max-Shift Algorithm for Approximate String Matching. In: Brodal, G.S., Frigioni, D., Marchetti-Spaccamela, A. (eds) Algorithm Engineering. WAE 2001. Lecture Notes in Computer Science, vol 2141. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44688-5_2

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  • DOI: https://doi.org/10.1007/3-540-44688-5_2

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-42500-7

  • Online ISBN: 978-3-540-44688-0

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