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Fixed Block Compression Boosting in FM-Indexes

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String Processing and Information Retrieval (SPIRE 2011)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7024))

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Abstract

A compressed full-text self-index occupies space close to that of the compressed text and simultaneously allows fast pattern matching and random access to the underlying text. Among the best compressed self-indexes, in theory and in practice, are several members of the FM-index family. In this paper, we describe new FM-index variants that combine nice theoretical properties, simple implementation and improved practical performance. Our main result is a new technique called fixed block compression boosting, which is a simpler and faster alternative to optimal compression boosting and implicit compression boosting used in previous FM-indexes.

Juha Kärkkäinen is supported by Academy of Finland grant 118653 (ALGODAN). Simon J. Puglisi is supported by a Newton Fellowship.

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References

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

    Google Scholar 

  2. Claude, F., Navarro, G.: Practical rank/Select queries over arbitrary sequences. In: Amir, A., Turpin, A., Moffat, A. (eds.) SPIRE 2008. LNCS, vol. 5280, pp. 176–187. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  3. Ferragina, P., Giancarlo, R., Manzini, G., Sciortino, M.: Boosting textual compression in optimal linear time. Journal of the ACM 52, 688–713 (2005)

    Article  MathSciNet  MATH  Google Scholar 

  4. Ferragina, P., González, R., Navarro, G., Venturini, R.: Compressed text indexes: From theory to practice. ACM Journal of Experimental Algorithmics 13, 1.12–1.31 (2009)

    MathSciNet  MATH  Google Scholar 

  5. Ferragina, P., Manzini, G.: Indexing compressed text. Journal of the ACM 52, 552–581 (2005)

    Article  MathSciNet  MATH  Google Scholar 

  6. Ferragina, P., Manzini, G., Mäkinen, V., Navarro, G.: Compressed representations of sequences and full-text indexes. ACM Transactions on Algorithms 3, Article 20 (2007)

    Article  MathSciNet  MATH  Google Scholar 

  7. Grossi, R., Gupta, A., Vitter, J.S.: High-order entropy-compressed text indexes. In: Proc. 14th Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 841–850. SIAM, Philadelphia (2003)

    Google Scholar 

  8. Grossi, R., Gupta, A., Vitter, J.S.: When indexing equals compression: experiments with compressing suffix arrays and applications. In: Proc. 15th Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 636–645. SIAM, Philadelphia (2004)

    Google Scholar 

  9. Kärkkäinen, J., Puglisi, S.J.: Medium-space algorithms for inverse bwt. In: de Berg, M., Meyer, U. (eds.) ESA 2010. LNCS, vol. 6346, pp. 451–462. Springer, Heidelberg (2010)

    Chapter  Google Scholar 

  10. Mäkinen, V., Navarro, G.: Succinct suffix arrays based on run-length encoding. Nordic Journal of Computing 12, 40–66 (2005)

    MathSciNet  MATH  Google Scholar 

  11. Mäkinen, V., Navarro, G.: Implicit compression boosting with applications to self-indexing. In: Ziviani, N., Baeza-Yates, R. (eds.) SPIRE 2007. LNCS, vol. 4726, pp. 229–241. Springer, Heidelberg (2007)

    Chapter  Google Scholar 

  12. Manzini, G.: An analysis of the Burrows-Wheeler transform. Journal of the ACM 48, 407–430 (2001)

    Article  MathSciNet  MATH  Google Scholar 

  13. Navarro, G., Mäkinen, V.: Compressed full-text indexes. ACM Computing Surveys 39 (2007)

    Google Scholar 

  14. Okanohara, D., Sadakane, K.: Practical entropy-compressed rank/select dictionary. In: Proc. Workshop on Algorithm Engineering and Experiments (ALENEX). SIAM, Philadelphia (2007)

    Google Scholar 

  15. Raman, R., Raman, V., Rao, S.S.: Succinct indexable dictionaries with applications to encoding k-ary trees, prefix sums and multisets. ACM Transactions on Algorithms 3 (2007)

    Google Scholar 

  16. Vigna, S.: Broadword implementation of rank/select queries. In: McGeoch, C.C. (ed.) WEA 2008. LNCS, vol. 5038, pp. 154–168. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of Helsinki, Finland

    Juha Kärkkäinen

  2. Department of Informatics, King’s College London, London, United Kingdom

    Simon J. Puglisi

Authors
  1. Juha Kärkkäinen
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  2. Simon J. Puglisi
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Editor information

Editors and Affiliations

  1. Università di Pisa, Italy

    Roberto Grossi

  2. Consiglio Nazionale delle Ricerche, Area della Ricerca di Pisa, Istituto di Scienza e Tecnologia dell’Informazione “Alessandro Faedo”, Via Giuseppe Moruzzi 1, 56124, Pisa, Italy

    Fabrizio Sebastiani  & Fabrizio Silvestri  & 

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Kärkkäinen, J., Puglisi, S.J. (2011). Fixed Block Compression Boosting in FM-Indexes. In: Grossi, R., Sebastiani, F., Silvestri, F. (eds) String Processing and Information Retrieval. SPIRE 2011. Lecture Notes in Computer Science, vol 7024. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-24583-1_18

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  • DOI: https://doi.org/10.1007/978-3-642-24583-1_18

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-24582-4

  • Online ISBN: 978-3-642-24583-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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