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European Symposium on Algorithms

ESA 2013: Algorithms – ESA 2013 pp 133–144Cite as

Versatile Succinct Representations of the Bidirectional Burrows-Wheeler Transform

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8125))

Abstract

We describe succinct and compact representations of the bidirectional bwt of a string s ∈ Σ* which provide increasing navigation power and a number of space-time tradeoffs. One such representation allows to extend a substring of s by one character from the left and from the right in constant time, taking O(|s| log |Σ|) bits of space. We then match the functions supported by each representation to a number of algorithms that traverse the nodes of the suffix tree of s, exploiting connections between the bwt and the suffix-link tree. This results in near-linear time algorithms for many sequence analysis problems (e.g. maximal unique matches), for the first time in succinct space.

This work was partially supported by Academy of Finland under grants 250345 (CoECGR) and 118653 (ALGODAN).

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Author information

Authors and Affiliations

  1. Helsinki Institute for Information Technology (HIIT), Department of Computer Science, University of Helsinki, Finland

    Djamal Belazzougui, Fabio Cunial, Juha Kärkkäinen & Veli Mäkinen

Authors
  1. Djamal Belazzougui
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  2. Fabio Cunial
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  3. Juha Kärkkäinen
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  4. Veli Mäkinen
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Editor information

Editors and Affiliations

  1. Department of Computer Science, Utrecht University, Princetonplein 5, 3584 CC, Utrecht, The Netherlands

    Hans L. Bodlaender

  2. Dipartimento di Ingegneria Civile e Ingegneria Informatica, Università di Roma “Tor Vergata”, via del Politecnico 1, 00133, Rome, Italy

    Giuseppe F. Italiano

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Belazzougui, D., Cunial, F., Kärkkäinen, J., Mäkinen, V. (2013). Versatile Succinct Representations of the Bidirectional Burrows-Wheeler Transform. In: Bodlaender, H.L., Italiano, G.F. (eds) Algorithms – ESA 2013. ESA 2013. Lecture Notes in Computer Science, vol 8125. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-40450-4_12

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  • DOI: https://doi.org/10.1007/978-3-642-40450-4_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-40449-8

  • Online ISBN: 978-3-642-40450-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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