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Succinct Suffix Arrays Based on Run-Length Encoding

  • Conference paper
Combinatorial Pattern Matching (CPM 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3537))

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Abstract

A succinct full-text self-index is a data structure built on a text T=t 1 t 2... t n , which takes little space (ideally close to that of the compressed text), permits efficient search for the occurrences of a pattern P=p 1 p 2... p m in T, and is able to reproduce any text substring, so the self-index replaces the text. Several remarkable self-indexes have been developed in recent years. They usually take O(nH 0) or O(nH k ) bits, being H k the kth order empirical entropy of T. The time to count how many times does P occur in T ranges from O(m) to O(mlog n).

We present a new self-index, called run-length FM-index (RLFM index), that counts the occurrences of P in T in O(m) time when the alphabet size is \(\sigma=O(\textrm{polylog}(n))\). The index requires nH k log2 σ + O(n) bits of space for small k. We then show how to implement the RLFM index in practice, and obtain in passing another implementation with different space-time tradeoffs. We empirically compare ours against the best existing implementations of other indexes and show that ours are fastest among indexes taking less space than the text.

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Author information

Authors and Affiliations

  1. AG Genominformatik, Technische Fakultät Universität Bielefeld, Germany

    Veli Mäkinen

  2. Center for Web Research Dept. of Computer Science, University of Chile,  

    Gonzalo Navarro

Authors
  1. Veli Mäkinen
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  2. Gonzalo Navarro
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Editor information

Editors and Affiliations

  1. Georgia Institute of Technology and Università di Padova,  

    Alberto Apostolico

  2. Université Paris-Est, France

    Maxime Crochemore

  3. School of Computer Science and Engineering, Seoul National University, 151-742, Seoul, Korea

    Kunsoo Park

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© 2005 Springer-Verlag Berlin Heidelberg

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Mäkinen, V., Navarro, G. (2005). Succinct Suffix Arrays Based on Run-Length Encoding. In: Apostolico, A., Crochemore, M., Park, K. (eds) Combinatorial Pattern Matching. CPM 2005. Lecture Notes in Computer Science, vol 3537. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11496656_5

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  • DOI: https://doi.org/10.1007/11496656_5

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-26201-5

  • Online ISBN: 978-3-540-31562-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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