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Linear-Time Construction of Compressed Suffix Arrays Using o(n log n)-Bit Working Space for Large Alphabets

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Book cover Combinatorial Pattern Matching (CPM 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3537))

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Abstract

The suffix array is a fundamental index data structure in string algorithms and bioinformatics, and the compressed suffix array (CSA) and theFM-index are its compressed versions. Many algorithms for constructing these index data structures have been developed. Recently, Hon et al. [11] proposed a construction algorithm using O(n ·loglog|Σ|) time and O(nlog|Σ|)-bit working space, which is the fastest algorithm using O(nlog|Σ|)-bit working space.

In this paper we give an efficient algorithm to construct the index data structures for large alphabets. Our algorithm constructs the suffix array, the CSA, and the FM-index using O(n) time and \(O(n \log|\Sigma| \log_{|\Sigma|}^{\;\alpha} n)\)-bit working space, where α = log3 2. Our algorithm takes less time and more space than Hon et al.’s algorithm. Our algorithm uses least working space among alphabet-independent linear-time algorithms.

This work was supported by the MOST Grant M6-0203-00-0039.

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References

  1. Burrows, M., Wheeler, D.J.: A block-sorting lossless data compression algorithm. Technical Report 124, Digital Equipment Corporation, Paolo Alto, California (1994)

    Google Scholar 

  2. Clark, D.R.: Compact Pat Trees. PhD thesis, University of Waterloo, Waterloo (1988)

    Google Scholar 

  3. Farach, M.: Optimal suffix tree construction with large alphabets. In: Proceedings of the 38th Annual IEEE Symposium on Foundations of Computer Science, pp. 137–143 (1997)

    Google Scholar 

  4. Farach-Colton, M., Ferragina, P., Muthukrishnan, S.: On the sorting-complexity of suffix tree construction. Journal of the ACM 47(6), 987–1011 (2000)

    Article  MATH  MathSciNet  Google Scholar 

  5. Ferragina, P., Manzini, G.: Opportunistic data structures with applications. In: Proceedings of the 41st Annual IEEE Symposium on Foundations of Computer Science, pp. 390–398 (2000)

    Google Scholar 

  6. Gonnet, G.H., Baeza-Yates, R., Snider, T.: New indices for text: Pat trees and pat arrays. In: Frakes, W.B., Baeza-Yates, R. (eds.) Information Retrieval: Data Structures & Algorithms, pp. 66–82. Prentice Hall, Englewood Cliffs (1992)

    Google Scholar 

  7. Grossi, R., Vitter, J.S.: Compressed suffix arrays and suffix trees with applications to text indexing and string matching. In: Proceedings of the 32nd Annual ACM Symposium on Theory of Computing, pp. 397–406 (2000)

    Google Scholar 

  8. Grossi, R., Vitter, J.S.: Compressed suffix arrays and suffix trees with applications to text indexing and string matching. Technical Report Submitted for publication (2001)

    Google Scholar 

  9. Gusfield, D.: An ”Increment-by-one” approach to suffix arrays and trees (manuscript, 1990)

    Google Scholar 

  10. Hon, W.K., Lam, T.W., Sadakane, K., Sung, W.K.: Constructing compressed suffix arrays with large alphabets. In: Ibaraki, T., Katoh, N., Ono, H. (eds.) ISAAC 2003. LNCS, vol. 2906, pp. 240–249. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  11. Hon, W.K., Sadakane, K., Sung, W.K.: Breaking a time-and-space barrier in constructing full-text indices. In: Proceedings of the 44th Annual IEEE Symposium on Foundations of Computer Science, pp. 251–260 (2003)

    Google Scholar 

  12. Kärkkäinen, J., Sanders, P.: Simple linear work suffix array construction. In: Baeten, J.C.M., Lenstra, J.K., Parrow, J., Woeginger, G.J. (eds.) ICALP 2003. LNCS, vol. 2719, pp. 943–955. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  13. Kim, D.K., Sim, J., Park, H., Park, K.: Linear-time construction of suffix arrays. In: Baeza-Yates, R., Chávez, E., Crochemore, M. (eds.) CPM 2003. LNCS, vol. 2676, pp. 186–199. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  14. Ko, P., Aluru, S.: Space-efficient linear time construction of suffix arrays. In: Baeza-Yates, R., Chávez, E., Crochemore, M. (eds.) CPM 2003. LNCS, vol. 2676, pp. 200–210. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  15. Lam, T.W., Sadakane, K., Sung, W.K., Yiu, S.M.: A space and time efficient algorithm for constructing compressed suffix arrays. In: Ibarra, O.H., Zhang, L. (eds.) COCOON 2002. LNCS, vol. 2387, pp. 401–410. Springer, Heidelberg (2002)

    Chapter  Google Scholar 

  16. Manber, U., Myers, G.: Suffix arrays: A new method for on-line string searches. SIAM Journal on Computing 22(5), 935–948 (1993)

    Article  MATH  MathSciNet  Google Scholar 

  17. Munro, J.I.: Tables. In: Chandru, V., Vinay, V. (eds.) FSTTCS 1996. LNCS, vol. 1180, pp. 37–42. Springer, Heidelberg (1996)

    Google Scholar 

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Author information

Authors and Affiliations

  1. School of Computer Science and Engineering, Seoul National University,  

    Joong Chae Na

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  1. Joong Chae Na
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Editors and Affiliations

  1. Georgia Institute of Technology and Università di Padova,  

    Alberto Apostolico

  2. Université Paris-Est, France

    Maxime Crochemore

  3. School of Computer Science and Engineering, Seoul National University, 151-742, Seoul, Korea

    Kunsoo Park

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© 2005 Springer-Verlag Berlin Heidelberg

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Na, J.C. (2005). Linear-Time Construction of Compressed Suffix Arrays Using o(n log n)-Bit Working Space for Large Alphabets. In: Apostolico, A., Crochemore, M., Park, K. (eds) Combinatorial Pattern Matching. CPM 2005. Lecture Notes in Computer Science, vol 3537. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11496656_6

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  • DOI: https://doi.org/10.1007/11496656_6

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-26201-5

  • Online ISBN: 978-3-540-31562-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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