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Simple Linear Work Suffix Array Construction

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Automata, Languages and Programming (ICALP 2003)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2719))

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Abstract

A suffix array represents the suffixes of a string in sorted order. Being a simpler and more compact alternative to suffix trees, it is an important tool for full text indexing and other string processing tasks. We introduce the skew algorithm for suffix array construction over integer alphabets that can be implemented to run in linear time using integer sorting as its only nontrivial subroutine:

  1. 1.

    recursively sort suffixes beginning at positions i mod 3 ≠ 0.

  2. 2.

    sort the remaining suffixes using the information obtained in step one.

  3. 3.

    merge the two sorted sequences obtained in steps one and two.

The algorithm is much simpler than previous linear time algorithms that are all based on the more complicated suffix tree data structure. Since sorting is a well studied problem, we obtain optimal algorithms for several other models of computation, e.g. external memory with parallel disks, cache oblivious, and parallel. The adaptations for BSP and EREW-PRAM are asymptotically faster than the best previously known algorithms.

Partially supported by the Future and Emerging Technologies programme of the EU under contract number IST-1999-14186(ALCOM-FT).

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Authors and Affiliations

  1. Max-Planck-Institut für Informatik, Stuhlsatzenhausweg 85, 66123, Saarbrücken, Germany

    Juha Kärkkäinen & Peter Sanders

Authors
  1. Juha Kärkkäinen
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  2. Peter Sanders
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Editors and Affiliations

  1. Dept. of Mathematics and Computer Science, Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands

    Jos C. M. Baeten

  2. School of Industrial and Systems Engineering, Georgia Institute of Technology, 765 Ferst Drive, Atlanta, GA, 30332-0205, USA

    Jan Karel Lenstra

  3. Department of Information Technology, Uppsala University, P.O. Box 337, 75105, Uppsala, Sweden

    Joachim Parrow

  4. Faculty of Electrical Engineering, Mathematics and Computer Science, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands

    Gerhard J. Woeginger

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Kärkkäinen, J., Sanders, P. (2003). Simple Linear Work Suffix Array Construction. In: Baeten, J.C.M., Lenstra, J.K., Parrow, J., Woeginger, G.J. (eds) Automata, Languages and Programming. ICALP 2003. Lecture Notes in Computer Science, vol 2719. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45061-0_73

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  • DOI: https://doi.org/10.1007/3-540-45061-0_73

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