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The Max-Shift Algorithm for Approximate String Matching

  • Costas S. Iliopoulos
  • Laurent Mouchard
  • Yoan J. Pinzon
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2141)

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.

Keywords

String algorithms approximate string matching dynamic programming edit-distance 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2001

Authors and Affiliations

  • Costas S. Iliopoulos
    • 1
    • 2
  • Laurent Mouchard
    • 3
    • 4
  • Yoan J. Pinzon
    • 1
    • 2
  1. 1.Dept. of Computer ScienceKing’s College LondonLondonEngland
  2. 2.School of ComputingCurtin University of Technology
  3. 3.ESA 6037: Dept. of Vegetal Physiology - ABISSUniversité de Rouen76821 Mont Saint Aignan CedexFrance
  4. 4.School of ComputingCurtin University of Technology

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