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Fast Algorithm for Partial Covers in Words

  • Tomasz Kociumaka
  • Solon P. Pissis
  • Jakub Radoszewski
  • Wojciech Rytter
  • Tomasz Waleń
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7922)

Abstract

A factor u of a word w is a cover of w if every position in w lies within some occurrence of u in w. A word w covered by u thus generalizes the idea of a repetition, that is, a word composed of exact concatenations of u. In this article we introduce a new notion of partial cover, which can be viewed as a relaxed variant of cover, that is, a factor covering at least a given number of positions in w. Our main result is an O(nlogn)-time algorithm for computing the shortest partial covers of a word of length n.

Keywords

Fast Algorithm Partial Cover Cover Index Union Operation Extra Node 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Tomasz Kociumaka
    • 1
  • Solon P. Pissis
    • 4
    • 5
  • Jakub Radoszewski
    • 1
  • Wojciech Rytter
    • 1
    • 2
  • Tomasz Waleń
    • 3
    • 1
  1. 1.Faculty of Mathematics, Informatics and MechanicsUniversity of WarsawWarsawPoland
  2. 2.Faculty of Mathematics and Computer ScienceCopernicus UniversityToruńPoland
  3. 3.Laboratory of Bioinformatics and Protein EngineeringInternational Institute of Molecular and Cell Biology in WarsawPoland
  4. 4.Laboratory of Molecular Systematics and Evolutionary Genetics, Florida Museum of Natural HistoryUniversity of FloridaUSA
  5. 5.Scientific Computing Group (Exelixis Lab & HPC Infrastructure)Heidelberg Institute for Theoretical Studies (HITS gGmbH)Germany

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