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Compact Suffix Array

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Combinatorial Pattern Matching (CPM 2000)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1848))

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Abstract

Suffix array is a data structure that can be used to index a large text file so that queries of its content can be answered quickly. Basically a suffix array is an array of all suffixes of the text in the lexicographic order. Whether or not a word occurs in the text can be answered in logarithmic time by binary search over the suffix array. In this work we present a method to compress a suffix array such that the search time remains logarithmic. Our experiments show that in some cases a suffix array can be compressed by our method such that the total space requirement is about half of the original.

A work supported by the Academy of Finland under grants 44449 and 22584.

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References

  1. R. Arnold and T. Bell, A corpus for the evaluation of lossless compression algorithms, Proceedings of the Data Compression Conference, 1997, pp. 201–210. http://corpus.canterbury.ac.nz

  2. A. Blumer, J. Blumer, D. Haussler, A. Ehrenfeucht, M. T. Chen, and J. Seiferas, The smallest automaton recognizing the subwords of a text, Theor. Sci., 40 (1985), pp. 31–55.

    Article  MATH  MathSciNet  Google Scholar 

  3. A. Blumer, J. Blumer, D. Haussler, and R. McConnell, Complete inverted files for efficient text retrieval and analysis, Journal of the ACM, 34:3 (1987), pp. 578–595.

    Article  MathSciNet  Google Scholar 

  4. A. Blumer, D. Haussler, A. Ehrenfeucht, Average sizes of suffix trees and dawgs, Discrete Applied Mathematics, 24 (1989), pp. 37–45.

    Article  MATH  MathSciNet  Google Scholar 

  5. M. Crochemore, Transducers and repetitions, Theor. Sci., 45 (1986), pp. 63–86.

    Article  MATH  MathSciNet  Google Scholar 

  6. M. Crochemore and Renaud Vérin, Direct Construction of Compact Directed Acyclic Word Graphs, In Proc. of the CPM, LNCS 1264 (1997), pp. 116–129.

    Google Scholar 

  7. Erdös and Rényi, On a new law of large numbers, J. Anal. Math. 22 (1970), pp. 103–111.

    Article  Google Scholar 

  8. G. H. Gonnet, R. A. Baeza-Yates, and T. Snider, Lexicographical indices for text: Inverted files vs. PAT trees, Technical Report OED-91-01, Centre for the New OED, University of Waterloo, 1991.

    Google Scholar 

  9. U. Manber and G. Myers, Suffix arrays: A new method for on-line string searches, SIAM J. Comput., 22(1993), pp. 935–948.

    Article  MATH  MathSciNet  Google Scholar 

  10. E. M. McCreight, A space economical suffix tree construction algorithm, Journal of the ACM, 23 (1976), pp. 262–272.

    Article  MATH  MathSciNet  Google Scholar 

  11. E. Ukkonen, On-line construction of suffix-trees, Algorithmica, 14 (1995), pp. 249–260.

    Article  MATH  MathSciNet  Google Scholar 

  12. M. S. Waterman, Introduction to Computational Biology, Chapman & Hall, University Press, Cambridge, UK, 1995, pp. 263–265.

    MATH  Google Scholar 

  13. P. Weiner, Linear pattern matching algorithms, In Proc. IEEE 14th Annual Symbosium on Switching and Automata Theory, 1973, pp. 1–11.

    Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of Helsinki, P.O Box26, Teollisuuskatu 23, FIN-00014, Finland

    Veli Mäkinen

Authors
  1. Veli Mäkinen
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Editor information

Editors and Affiliations

  1. Dipartimento di Matematica ed Applicazioni, Universitá die Palermo, Via Archirafi 34, 90123, Palermo, Italy

    Raffaele Giancarlo

  2. Centre de recherches mathématiques, Université de Montréal, CP 6128, succursale Centre-Ville, Montréal, Québec, Canada, H3C 3J7

    David Sankoff

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© 2000 Springer-Verlag Berlin Heidelberg

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Mäkinen, V. (2000). Compact Suffix Array. In: Giancarlo, R., Sankoff, D. (eds) Combinatorial Pattern Matching. CPM 2000. Lecture Notes in Computer Science, vol 1848. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45123-4_26

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  • DOI: https://doi.org/10.1007/3-540-45123-4_26

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-67633-1

  • Online ISBN: 978-3-540-45123-5

  • eBook Packages: Springer Book Archive

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