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Alphabet-Independent Algorithms for Finding Context-Sensitive Repeats in Linear Time

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String Processing and Information Retrieval (SPIRE 2014)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8799))

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Abstract

The identification of repetitive sequences (repeats) is an essential component of genome sequence analysis, and there are dozens of algorithms that search for exact or approximate repeats. The notions of maximal and supermaximal (exact) repeats have received special attention, and it is possible to simultaneously compute them on index data structures like the suffix tree or the enhanced suffix array. Very recently, this research has been extended in two directions. Gallé and Tealdi devised an alphabet-independent linear-time algorithm that finds all context-diverse repeats (which subsume maximal and supermaximal repeats as special cases), while Taillefer and Miller gave a quadratic-time algorithm that simultaneously computes and classifies maximal, near-supermaximal, and supermaximal repeats. In this paper, we provide new alphabet-independent linear-time algorithms for both tasks.

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Authors and Affiliations

  1. Institute of Theoretical Computer Science, University of Ulm, D-89069, Ulm, Germany

    Enno Ohlebusch & Timo Beller

Authors
  1. Enno Ohlebusch
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  2. Timo Beller
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Editors and Affiliations

  1. Instituto de Computação, Universidade Federal do Amazonas, 6200, Manaus, Brazil

    Edleno Moura

  2. King’s College London, UK

    Maxime Crochemore

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Ohlebusch, E., Beller, T. (2014). Alphabet-Independent Algorithms for Finding Context-Sensitive Repeats in Linear Time. In: Moura, E., Crochemore, M. (eds) String Processing and Information Retrieval. SPIRE 2014. Lecture Notes in Computer Science, vol 8799. Springer, Cham. https://doi.org/10.1007/978-3-319-11918-2_12

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  • DOI: https://doi.org/10.1007/978-3-319-11918-2_12

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-11917-5

  • Online ISBN: 978-3-319-11918-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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