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Compressed Suffix Trees for Repetitive Texts

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String Processing and Information Retrieval (SPIRE 2012)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7608))

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Abstract

We design a new compressed suffix tree specifically tailored to highly repetitive text collections. This is particularly useful for sequence analysis on large collections of genomes of the close species. We build on an existing compressed suffix tree that applies statistical compression, and modify it so that it works on the grammar-compressed version of the longest common prefix array, whose differential version inherits much of the repetitiveness of the text.

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

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Author information

Authors and Affiliations

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

    Andrés Abeliuk & Gonzalo Navarro

  2. Instituto de Filosofía y Ciencias de la Complejidad, IFICC, University of Chile, Chile

    Andrés Abeliuk

Authors
  1. Andrés Abeliuk
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  2. Gonzalo Navarro
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Editor information

Editors and Affiliations

  1. Information Technologies Research Group, Universidad Autónoma de Bucaramanga, Bucaramanga, Colombia

    Liliana Calderón-Benavides

  2. Information Technologies and Research Group, Universidad Autónoma de Bucaramanga, Bucaramanga, Colombia

    Cristina González-Caro

  3. School of Physics and Mathematics, Universidad Michoacana, Edificio ”B”, Ciudad Universitaria,, 58000, Morelia, Mexico

    Edgar Chávez

  4. Department of Computer Science, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, Pampulha, 31270-010, Belo Horizonte, Brazil

    Nivio Ziviani

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© 2012 Springer-Verlag Berlin Heidelberg

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Abeliuk, A., Navarro, G. (2012). Compressed Suffix Trees for Repetitive Texts. In: Calderón-Benavides, L., González-Caro, C., Chávez, E., Ziviani, N. (eds) String Processing and Information Retrieval. SPIRE 2012. Lecture Notes in Computer Science, vol 7608. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-34109-0_5

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  • DOI: https://doi.org/10.1007/978-3-642-34109-0_5

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-34108-3

  • Online ISBN: 978-3-642-34109-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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