Approximate string matching with don't care characters

  • Tatsuya Akutsu
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 807)


This paper presents parallel and serial approximate matching algorithms for strings with don't care characters. They are based on Landau and Vishkin's approximate string matching algorithm and Fisher and Paterson's exact string matching algorithm with don't care characters. The serial algorithm works in O(√kmn log¦Σ¦ log2m/k log log m/k) time, and the parallel algorithm works in O(k log m) time using O(√m/kn log ¦Σ¦ log m/k log log m/k) Processors on a CRCW-PRAM, where n denotes the length of a text string, m denotes the length of a pattern string, k denotes the maximum number of differences, and ∑ denotes the alphabet (i.e. the set of characters). Several extensions are also described.


approximate string matching don't care characters sequence analysis 


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Copyright information

© Springer-Verlag Berlin Heidelberg 1994

Authors and Affiliations

  • Tatsuya Akutsu
    • 1
  1. 1.Mechanical Engineering LaboratoryIbarakiJapan

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