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Practical Variable Length Gap Pattern Matching

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Experimental Algorithms (SEA 2016)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 9685))

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Abstract

Solving the problem of reporting all occurrences of patterns containing variable length gaps in an input text T efficiently is important for various applications in a broad range of domains such as Bioinformatics or Natural Language Processing. In this paper we present an efficient solution for static inputs which utilizes the wavelet tree of the suffix array. The algorithm partially traverses the wavelet tree to find matches and can be easily adapted to several variants of the problem. We explore the practical properties of our solution in an experimental study where we compare to online and semi-indexed solutions using standard datasets. The experiments show that our approach is the best choice for searching patterns with many gaps in large texts.

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Notes

  1. 1.

    I.e. any two match tuples \({\langle }i_0\ldots i_{k-1}{\rangle }\) and \({\langle }i'_0\ldots i'_{k-1}{\rangle }\) spanning the intervals \([i_0,i_{k-1}+m_{k-1}-1]\) and \([i'_0,i'_{k-1}+m_{k-1}-1]\) do not overlap.

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Acknowledgement

We are grateful to Timo Bingmann for profiling our initial implementation. This work was supported under the Australian Research Council’s Discovery Projects scheme (project DP140103256) and Deutsche Forschungsgemeinschaft.

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Authors and Affiliations

  1. Institute of Theoretical Informatics, Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany

    Johannes Bader & Simon Gog

  2. Department of Computing and Information Systems, The University of Melbourne, VIC, 3010, Australia

    Matthias Petri

Authors
  1. Johannes Bader
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  2. Simon Gog
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  3. Matthias Petri
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Corresponding author

Correspondence to Simon Gog .

Editor information

Editors and Affiliations

  1. Amazon.com, Inc., Palo Alto, California, USA

    Andrew V. Goldberg

  2. Russian Academy of Sciences, St. Petersburg, Russia

    Alexander S. Kulikov

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Bader, J., Gog, S., Petri, M. (2016). Practical Variable Length Gap Pattern Matching. In: Goldberg, A., Kulikov, A. (eds) Experimental Algorithms. SEA 2016. Lecture Notes in Computer Science(), vol 9685. Springer, Cham. https://doi.org/10.1007/978-3-319-38851-9_1

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  • DOI: https://doi.org/10.1007/978-3-319-38851-9_1

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-38850-2

  • Online ISBN: 978-3-319-38851-9

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