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Sampling the Suffix Array with Minimizers

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String Processing and Information Retrieval (SPIRE 2015)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 9309))

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  • International Symposium on String Processing and Information Retrieval

Abstract

Sampling (evenly) the suffixes from the suffix array is an old idea trading the pattern search time for reduced index space. A few years ago Claude et al. showed an alphabet sampling scheme allowing for more efficient pattern searches compared to the sparse suffix array, for long enough patterns. A drawback of their approach is the requirement that sought patterns need to contain at least one character from the chosen subalphabet. In this work we propose an alternative suffix sampling approach with only a minimum pattern length as a requirement, which seems more convenient in practice. Experiments show that our algorithm achieves competitive time-space tradeoffs on most standard benchmark data. As a side result, we show that \(n'\) arbitrarily selected suffixes from a text of length n, where \(n' < n\), over an integer alphabet, can be sorted in O(n) time using \(O(n')\) words of space.

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Author information

Authors and Affiliations

  1. Institute of Applied Computer Science, Lodz University of Technology, Al. Politechniki 11, 90–924, Łódź, Poland

    Szymon Grabowski & Marcin Raniszewski

Authors
  1. Szymon Grabowski
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  2. Marcin Raniszewski
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Corresponding author

Correspondence to Szymon Grabowski .

Editor information

Editors and Affiliations

  1. King's College London, London, United Kingdom

    Costas Iliopoulos

  2. University of Helsinki, Helsinki, Finland

    Simon Puglisi

  3. University College London, London, United Kingdom

    Emine Yilmaz

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Grabowski, S., Raniszewski, M. (2015). Sampling the Suffix Array with Minimizers. In: Iliopoulos, C., Puglisi, S., Yilmaz, E. (eds) String Processing and Information Retrieval. SPIRE 2015. Lecture Notes in Computer Science(), vol 9309. Springer, Cham. https://doi.org/10.1007/978-3-319-23826-5_28

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  • DOI: https://doi.org/10.1007/978-3-319-23826-5_28

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-23825-8

  • Online ISBN: 978-3-319-23826-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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