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A fast filtration algorithm for the substring matching problem

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Combinatorial Pattern Matching (CPM 1993)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 684))

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Abstract

Given a text of length n and a query of length q we present an algorithm for finding all locations of m-tuples in the text and in the query that differ by at most K mismatches. This problem is motivated by the dot-matrix constructions for sequence comparison and optimal oligonucleotide probe selection routinely used in molecular biology. In the case q = m the problem coincides with the classical approximate string matching with k mismatches problem. We present a new approach to this problem based on multiple filtration which may have advantages over some sophisticated and theoretically efficient methods that have been proposed. This paper describes a two-stage process. The first stage (multiple filtration) uses a new technique to preselect roughly similar m-tuples. The second stage compares these m-tuples using an accurate method. We demonstrate the advantages of multiple filtration in comparison with other techniques for approximate pattern matching.

The research was supported in part by the National Science Foundation (DMS 90-05833) and the National Institute of Health (GM-36230). This paper was written when P.A.P. was at the Department of Mathematics, University of Southern California.

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Author information

Authors and Affiliations

  1. Computer Science Department, The Pennsylvania State University, 16802, University Park, PA

    Pavel A. Pevzner

  2. Departments of Mathematics and of Molecular Biology, University of Southern California, 90089-1113, Los Angeles, California

    Michael S. Waterman

Authors
  1. Pavel A. Pevzner
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  2. Michael S. Waterman
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Editor information

Alberto Apostolico Maxime Crochemore Zvi Galil Udi Manber

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© 1993 Springer-Verlag Berlin Heidelberg

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Pevzner, P.A., Waterman, M.S. (1993). A fast filtration algorithm for the substring matching problem. In: Apostolico, A., Crochemore, M., Galil, Z., Manber, U. (eds) Combinatorial Pattern Matching. CPM 1993. Lecture Notes in Computer Science, vol 684. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0029806

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  • DOI: https://doi.org/10.1007/BFb0029806

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-56764-6

  • Online ISBN: 978-3-540-47732-7

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