New Bit-Parallel Indel-Distance Algorithm

  • Heikki Hyyrö
  • Yoan Pinzon
  • Ayumi Shinohara
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3503)


The task of approximate string matching is to find all locations at which a pattern string p of length m matches a substring of a text string t of length n with at most k differences. It is common to use Levenshtein distance [5], which allows the differences to be single-character insertions, deletions, substitutions. Recently, in [3], the IndelMYE, IndelWM and IndelBYN algorithms where introduced as modified version of the bit-parallel algorithms of Myers [6], Wu&Manber [10] and Baeza-Yates&Navarro [1], respectively. These modified versions where made to support the indel distance (only single-character insertions and/or deletions are allowed). In this paper we present an improved version of IndelMYE that makes a better use of the bit-operations and runs 24.5 percent faster in practice. In the end we present a complete set of experimental results to support our findings.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Heikki Hyyrö
    • 1
  • Yoan Pinzon
    • 2
  • Ayumi Shinohara
    • 1
    • 3
  1. 1.PRESTOJapan Science and Technology Agency (JST)Japan
  2. 2.Department of Computer ScienceKing’s CollegeLondonUK
  3. 3.Department of InformaticsKyushu University 33FukuokaJapan

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