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Indexing Compressed Text

  • Reference work entry
Encyclopedia of Database Systems

Synonyms

Compressed full-text indexing; Compressed suffix array Compressed suffix tree Compressed and searchable data format

Definition

Given a text T[1,n], the Compressed Text Indexing problem requires to building an indexing data structure over T that takes space close to the empirical entropy of the input text and answers queries on the occurrences of an arbitrary pattern P[1,p] in T without any significant slowdown with respect to uncompressed indexes. There are three main queries:count(P), that returns the number of pattern occurrences in T, locate(P), that returns the starting positions of all pattern occurrences in T, and extract(i, j), that retrieves the substring T[i, j].

Historical Background

String processing and searching tasks are at the core of modern web search, information retrieval (IR), data base and data mining applications. Most of text manipulations required by these applications involve, sooner or later, searching those (long) texts for (short) patterns or accessing...

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Recommended Reading

  1. Arroyuelo D., Navarro G., and Sadakane K. Reducing the space requirement of LZ-index. In Proc. 17th Annual Symposium on Combinatorial Pattern Matching, pp. 319–330.2006,

    Google Scholar 

  2. Barbay J., He M., Munro J.I., and Srinivasa Rao S. Succinct indexes for string, binary relations and multi-labeled trees. In Proc. 18th Annual ACM -SIAM Symp. on Discrete Algorithms, 2007, pp. 680–689.

    Google Scholar 

  3. Bender M.A., Farach-Colton M., and Kuszmaul B.C. Cache-oblivious string B-trees. In Proc. 25th ACM SIGACT-SIGMOD-SIGART Symp. on Principles of Database Systems, 2006, pp. 233–242.

    Google Scholar 

  4. Burrows M. and Wheeler D. A block sorting lossless data compression algorithm. Technical Report 124, Digital Equipment Corporation, 1994.

    Google Scholar 

  5. Ferragina P. String Search in External Memory: Data Structures and Algorithms, In Handbook of Computational Molecular Biology, Chapman & Hall, London, 2005.

    Google Scholar 

  6. Ferragina P., González R., Navarro G., and Venturini R. Compressed Text Indexes: From Theory to Practice, J. Exp. Algorithmics, 13:1.12–1.31, 2009.

    Google Scholar 

  7. Ferragina P. and Grossi R. The String B-tree: A new data structure for string search in external memory and its applications. J. ACM, 46(2):236–280, 1999.

    Article  MathSciNet  MATH  Google Scholar 

  8. Ferragina P., Grossi R., Gupta A., Shah R., and Vitter J.S. On searching compressed string collections cache-obliviously. In Proc. 27th ACM SIGACT-SIGMOD-SIGART Symp. on Principles of Database Systems, 2008, pp. 181–190.

    Google Scholar 

  9. Ferragina P. and Manzini G. Indexing compressed text. J. ACM, 52(4):552–581, 2005.

    Article  MathSciNet  Google Scholar 

  10. Ferragina P., Manzini G., Mäkinen V., and Navarro G. Compressed representations of sequences and full-text indexes. ACM Trans. Algorithms, 3(2), 2007.

    Google Scholar 

  11. Ferragina P. and Venturini R. Compressed permuterm index. In Proc. 33rd Annual Int. ACM SIGIR Conf. on Research and Development in Information Retrieval, 2007, pp. 535–542.

    Google Scholar 

  12. Grossi R., Gupta A., and Vitter J.S. High-order entropy-compressed text indexes. In Proc. 14th Annual ACM-SIAM Symp. on Discrete Algorithms, 2003, pp. 841–850.

    Google Scholar 

  13. Grossi R. and Vitter J.S. Compressed suffix arrays and suffix trees with applications to text indexing and string matching. SIAM J. Comput., 35(2):378–407, 2005.

    Article  MathSciNet  MATH  Google Scholar 

  14. Navarro G. and Mäkinen V. Compressed full-text indexes. ACM Comput. Surv., 39(1), 2007.

    Google Scholar 

  15. Sadakane K. Compressed suffix trees with full functionality. Theory Comput. Syst., 41(4):589–607, 2007.

    Article  MathSciNet  MATH  Google Scholar 

  16. Sadakane K. New text indexing functionalities of the compressed suffix arrays. J. Algorithms, 48(2):294–413, 2007.

    Article  MathSciNet  Google Scholar 

  17. Sadakane K. Succinct data structures for flexible text retrieval systems. J. Discrete Algorithms, 5(1):12–22, 2007.

    Article  MathSciNet  MATH  Google Scholar 

  18. Tam S.L., Wong C.K., Lam T.W., Sung W.K., and Yiu S.M. Compressed indexing and local alignment of DNA. Bioinformatics, 24(6):791–797, 2008.

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. University of Pisa, Pisa, Italy

    Paolo Ferragina & Rossano Venturini

Authors
  1. Paolo Ferragina
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  2. Rossano Venturini
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Editor information

Editors and Affiliations

  1. College of Computing, Georgia Institute of Technology, 266 Ferst Drive, 30332-0765, Atlanta, GA, USA

    LING LIU (Professor) (Professor)

  2. Database Research Group David R. Cheriton School of Computer Science, University of Waterloo, 200 University Avenue West, N2L 3G1, Waterloo, ON, Canada

    M. TAMER ÖZSU (Professor and Director, University Research Chair) (Professor and Director, University Research Chair)

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Ferragina, P., Venturini, R. (2009). Indexing Compressed Text. In: LIU, L., ÖZSU, M.T. (eds) Encyclopedia of Database Systems. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-39940-9_1144

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