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Space-Efficient Computation of Maximal and Supermaximal Repeats in Genome Sequences

  • Timo Beller
  • Katharina Berger
  • Enno Ohlebusch
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7608)

Abstract

The identification of repetitive sequences (repeats) is an essential component of genome sequence analysis, and the notions of maximal and supermaximal repeats capture all exact repeats in a genome in a compact way. Very recently, Külekci et al. (Computational Biology and Bioinformatics, 2012) developed an algorithm for finding all maximal repeats that is very space-efficient because it uses the Burrows-Wheeler transform and wavelet trees. In this paper, we present a new space-efficient algorithm for finding maximal repeats in massive data that outperforms their algorithm both in theory and practice. The algorithm is not confined to this task, it can also be used to find all supermaximal repeats or to solve other problems space-efficiently.

Keywords

Maximal Repeat Wavelet Tree Lossless Data Compression Real Runtime True List 
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 2012

Authors and Affiliations

  • Timo Beller
    • 1
  • Katharina Berger
    • 1
  • Enno Ohlebusch
    • 1
  1. 1.Institute of Theoretical Computer ScienceUniversity of UlmUlmGermany

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