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Annual Symposium on Combinatorial Pattern Matching

CPM 2013: Combinatorial Pattern Matching pp 201–210Cite as

External Memory Generalized Suffix and LCP Arrays Construction

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7922))

Abstract

A suffix array is a data structure that, together with the LCP array, allows solving many string processing problems in a very efficient fashion. In this article we introduce eGSA, the first external memory algorithm to construct both generalized suffix and LCP arrays for sets of strings. Our algorithm relies on a combination of buffers, induced sorting and a heap. Performance tests with real DNA sequence sets of size up to 8.5 GB showed that eGSA can indeed be applied to sets of large sequences with efficient running time on a low-cost machine. Compared to the algorithm that most closely resembles eGSA purpose, eSAIS, eGSA reduced the time spent to construct the arrays by a factor of 2.5−4.8.

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Author information

Authors and Affiliations

  1. Institute of Mathematics and Computer Science, University of São Paulo, São Carlos, SP, Brazil

    Felipe A. Louza & Cristina Dutra De Aguiar Ciferri

  2. Institute of Computing, University of Campinas, Campinas, SP, Brazil

    Guilherme P. Telles

Authors
  1. Felipe A. Louza
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  2. Guilherme P. Telles
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  3. Cristina Dutra De Aguiar Ciferri
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Editor information

Editors and Affiliations

  1. Fakultät für Informatik, Institut für Theoretische Informatik, Karlsruhe Institut für Technology, Am Fasanengarten 5, 76131, Karlsruhe, Germany

    Johannes Fischer

  2. Karlsruhe Institute of Technology, Germany

    Peter Sanders

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Louza, F.A., Telles, G.P., Ciferri, C.D.D.A. (2013). External Memory Generalized Suffix and LCP Arrays Construction. In: Fischer, J., Sanders, P. (eds) Combinatorial Pattern Matching. CPM 2013. Lecture Notes in Computer Science, vol 7922. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38905-4_20

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  • DOI: https://doi.org/10.1007/978-3-642-38905-4_20

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-38904-7

  • Online ISBN: 978-3-642-38905-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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