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Practical Compressed Suffix Trees

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Experimental Algorithms (SEA 2010)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6049))

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Abstract

The suffix tree is an extremely important data structure for stringology, with a wealth of applications in bioinformatics. Classical implementations require much space, which renders them useless for large problems. Recent research has yielded two implementations offering widely different space-time tradeoffs. However, each of them has practicality problems regarding either space or time requirements. In this paper we implement a recent theoretical proposal and show it yields an extremely interesting structure that lies in between, offering both practical times and affordable space. The implementation is by no means trivial and involves significant algorithm engineering.

Partially funded by Millennium Institute of Cell Dynamics and Biotechnology (ICDB), Grant ICM P05-001-F, Mideplan, and by Fondecyt Grant 1-080019, Chile.

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of Chile, Chile

    Rodrigo Cánovas & Gonzalo Navarro

Authors
  1. Rodrigo Cánovas
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  2. Gonzalo Navarro
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Editor information

Editors and Affiliations

  1. Department of Mathematics and Applications, University of Napoli Federico II, Compl. MSA, Via Cintia, 80126, Napoli, Italy

    Paola Festa

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Cánovas, R., Navarro, G. (2010). Practical Compressed Suffix Trees. In: Festa, P. (eds) Experimental Algorithms. SEA 2010. Lecture Notes in Computer Science, vol 6049. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13193-6_9

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  • DOI: https://doi.org/10.1007/978-3-642-13193-6_9

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-13192-9

  • Online ISBN: 978-3-642-13193-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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