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Longest Repeats with a Block of Don’t Cares

  • Maxime Crochemore
  • Costas S. Iliopoulos
  • Manal Mohamed
  • Marie-France Sagot
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2976)

Abstract

We introduce an algorithm for extracting all longest repeats with k don’t cares from a given sequence. Such repeats are composed of two parts separated by a block of k don’t care symbols. The algorithm uses suffix trees to fulfill this task and relies on the ability to answer the lowest common ancestor queries in constant time. It requires O(n log n) time in the worst-case.

Keywords

Combinatorial Problems String Repeat Extraction Don’t Care Suffix Tree Lowest Common Ancestor Efficient Merging 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Maxime Crochemore
    • 1
    • 2
  • Costas S. Iliopoulos
    • 2
  • Manal Mohamed
    • 2
  • Marie-France Sagot
    • 3
  1. 1.Institut Gaspard-MongeUniversity of Marne-la-ValléeMarne-la-Vallée CEDEX 2France
  2. 2.Department of Computer ScienceKing’s College LondonLondonEngland
  3. 3.Inria Rhône-Alpes, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité Claude BernardVilleurbanne cedexFrance

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