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A Constant-Space Comparison-Based Algorithm for Computing the Burrows–Wheeler Transform

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Combinatorial Pattern Matching (CPM 2013)

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

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Abstract

We introduce the problem of computing the Burrows– Wheeler Transform (\(\small\mathrm{BWT}\)) using just O(1) additional space. Our in-place algorithm does not need the explicit storage for the suffix sort array and the output array, as typically required in previous work. It relies on the combinatorial properties of the \(\small\mathrm{BWT}\), and runs in O(n 2) time in the comparison model using O(1) extra memory cells, apart from the array of n cells storing the n characters of the input text. We also discuss some time-space trade-offs for the inverse algorithm to obtain the text from the given \(\small\mathrm{BWT}\).

The work of the third author has been supported by the Academy of Finland grant 118653 (ALGODAN). The work of the fourth author has been partially supported by the National Science Foundation Award 0904246, Israel Science Foundation grant 347/09, Yahoo, Grant No. 2008217 from the United States-Israel Binational Science Foundation (BSF) and DFG.

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Author information

Authors and Affiliations

  1. King’s College London, UK

    Maxime Crochemore

  2. Dipartimento di Informatica, Università di Pisa, Italy

    Roberto Grossi

  3. Department of Computer Science, University of Helsinki, Finland

    Juha Kärkkäinen

  4. Department of Computer Science, University of Haifa, Israel

    Gad M. Landau

  5. Department of Computer Science and Engineering, NYU-Poly, Brooklyn, NY, USA

    Gad M. Landau

Authors
  1. Maxime Crochemore
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  2. Roberto Grossi
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  3. Juha Kärkkäinen
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  4. Gad M. Landau
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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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Crochemore, M., Grossi, R., Kärkkäinen, J., Landau, G.M. (2013). A Constant-Space Comparison-Based Algorithm for Computing the Burrows–Wheeler Transform. 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_9

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  • DOI: https://doi.org/10.1007/978-3-642-38905-4_9

  • 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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