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Compressed Suffix Trees for Repetitive Texts

  • Conference paper

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

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.

Keywords

  • Compression Method
  • Text Collection
  • Lower Common Ancestor
  • Statistical Compressibility
  • Range Minimum Query

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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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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

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