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Suffix Arrays on Words

  • Conference paper
Combinatorial Pattern Matching (CPM 2007)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4580))

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Abstract

Surprisingly enough, it is not yet known how to build directly a suffix array that indexes just the k positions at word-boundaries of a text T[1,n], taking O(n) time and O(k) space in addition to T. We propose a class-note solution to this problem that achieves such optimal time and space bounds. Word-based versions of indexes achieving the same time/space bounds were already known for suffix trees [1,2] and (compact) DAWGs [3,4]. Our solution inherits the simplicity and efficiency of suffix arrays, with respect to such other word-indexes, and thus it foresees applications in word-based approaches to data compression [5] and computational linguistics [6]. To support this, we have run a large set of experiments showing that word-based suffix arrays may be constructed twice as fast as their full-text counterparts, and with a working space as low as 20%. The space reduction of the final word-based suffix array impacts also in their query time (i.e. less random access binary-search steps!), being faster by a factor of up to 3.

The first author has been partially supported by the Italian MIUR grant Italy-Israel FIRB “Pattern Discovery Algorithms in Discrete Structures, with Applications to Bioinformatics”, and by the Yahoo! Research grant on “Data compression and indexing in hierarchical memories”. The second autor has been partially funded by the German Research Foundation (DFG, Bioinformatics Initiative).

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Authors and Affiliations

  1. Dipartimento di Informatica, University of Pisa,  

    Paolo Ferragina

  2. Institut für Informatik, Ludwig-Maximilians-Universität München,  

    Johannes Fischer

Authors
  1. Paolo Ferragina
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  2. Johannes Fischer
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Bin Ma Kaizhong Zhang

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Ferragina, P., Fischer, J. (2007). Suffix Arrays on Words. In: Ma, B., Zhang, K. (eds) Combinatorial Pattern Matching. CPM 2007. Lecture Notes in Computer Science, vol 4580. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73437-6_33

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  • DOI: https://doi.org/10.1007/978-3-540-73437-6_33

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-73436-9

  • Online ISBN: 978-3-540-73437-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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