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International Symposium on String Processing and Information Retrieval

SPIRE 2014: String Processing and Information Retrieval pp 179–190Cite as

Indexed Matching Statistics and Shortest Unique Substrings

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8799))

Abstract

The unidirectional and bidirectional matching statistics between two strings s and t on alphabet Σ, and the shortest unique substrings of a single string t, are the cornerstone of a number of large-scale genome analysis applications, and they encode nontrivial structural properties of s and t. In this paper we compute for the first time the matching statistics between s and t in O((|s| + |t|)log|Σ|) time and in O(|s|log|Σ|) bits of space, circumventing the need for computing the depths of suffix tree nodes that characterized previous approaches. Symmetrically, we compute for the first time the shortest unique substrings of a string t in O(|t|log|Σ|) time and in O(|t|log|Σ|) bits of space. A key component of our methods is an encoding of both the unidirectional and the bidirectional statistics that takes 2|t| + o(|t|) bits of space and that allows constant-time access to every position.

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Author information

Authors and Affiliations

  1. Helsinki Institute for Information Technology (HIIT), Department of Computer Science, University of Helsinki, Finland

    Djamal Belazzougui & Fabio Cunial

Authors
  1. Djamal Belazzougui
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  2. Fabio Cunial
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Editor information

Editors and Affiliations

  1. Instituto de Computação, Universidade Federal do Amazonas, 6200, Manaus, Brazil

    Edleno Moura

  2. King’s College London, UK

    Maxime Crochemore

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© 2014 Springer International Publishing Switzerland

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Cite this paper

Belazzougui, D., Cunial, F. (2014). Indexed Matching Statistics and Shortest Unique Substrings. In: Moura, E., Crochemore, M. (eds) String Processing and Information Retrieval. SPIRE 2014. Lecture Notes in Computer Science, vol 8799. Springer, Cham. https://doi.org/10.1007/978-3-319-11918-2_18

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  • DOI: https://doi.org/10.1007/978-3-319-11918-2_18

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-11917-5

  • Online ISBN: 978-3-319-11918-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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