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Annual Symposium on Combinatorial Pattern Matching

CPM 1993: Combinatorial Pattern Matching pp 228–242Cite as

Approximate string-matching over suffix trees

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

Abstract

The classical approximate string-matching problem of finding the locations of approximate occurrences P′ of pattern string P in text string T such that the edit distance between P and P′ is ≤ k is considered. We concentrate on the special case in which T is available for preprocessing before the searches with varying P and k. It is shown how the searches can be done fast using the suffix tree of T augmented with the suffix links as the preprocessed form of T and applying dynamic programming over the tree. Three variations of the search algorithm are developed with running times O(mq + n), O(mq log q + size of the output), and O(m 2 q + size of the output). Here n = ¦T¦, m = ¦P¦, and q varies depending on the problem instance between 0 and n. In the case of the unit cost edit distance it is shown that q = O(min(n, m k+1¦∑¦k)) where ∑ is the alphabet.

This work was supported by the Academy of Finland and by the Alexander von Humboldt Foundation (Germany).

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of Helsinki, University of Helsinki, P. O. Box 26, SF-00014, Finland

    Esko Ukkonen

Authors
  1. Esko Ukkonen
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Alberto Apostolico Maxime Crochemore Zvi Galil Udi Manber

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© 1993 Springer-Verlag Berlin Heidelberg

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Ukkonen, E. (1993). Approximate string-matching over suffix trees. 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/BFb0029808

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  • DOI: https://doi.org/10.1007/BFb0029808

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-56764-6

  • Online ISBN: 978-3-540-47732-7

  • eBook Packages: Springer Book Archive

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