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Succinct Gapped Suffix Arrays

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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

Gapped suffix arrays (also known as bi-factor arrays) were recently presented for approximate searching under the Hamming distance. These structures can be used to find occurrences of a pattern P, where the characters inside a gap do not have to match. This paper describes a succinct representation of gapped suffix arrays.

Supported by FCT through projects TAGS PTDC/EIA-EIA/112283/2009, HELIX PTDC/EEA-ELC/113999/2009 and the PIDDAC Program funds (INESC-ID multiannual funding).

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References

  1. Burrows, M., Wheeler, D.J.: A block-sorting lossless data compression algorithm. Technical report, Digital SRC Research Report (1994)

    Google Scholar 

  2. Crochemore, M., Hancart, C., Lecroq, T.: Algorithms on Strings, 392 pages. Cambridge University Press, Cambridge (2007)

    Book  MATH  Google Scholar 

  3. Crochemore, M., Tischler, G.: The gapped suffix array: A new index structure for fast approximate matching. In: Chavez, E., Lonardi, S. (eds.) SPIRE 2010. LNCS, vol. 6393, pp. 359–364. Springer, Heidelberg (2010)

    Chapter  Google Scholar 

  4. Ferragina, P., Manzini, G., Mäkinen, V., Navarro, G.: An alphabet-friendly FM-index. In: Apostolico, A., Melucci, M. (eds.) SPIRE 2004. LNCS, vol. 3246, pp. 150–160. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  5. Gagie, T., Puglisi, S.J., Turpin, A.: Range quantile queries: Another virtue of wavelet trees. In: Karlgren, J., Tarhio, J., Hyyrö, H. (eds.) SPIRE 2009. LNCS, vol. 5721, pp. 1–6. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

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

    Google Scholar 

  7. Jacobson, G.: Space-efficient Static Trees and Graphs. In: Foundations of Computer Science, pp. 549–554 (1989)

    Google Scholar 

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

    Chapter  Google Scholar 

  9. Peterlongo, P., Allali, J., Sagot, M.-F.: Indexing gapped-factors using a tree. Int. J. Found. Comput. Sci. 19(1), 71–87 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  10. Peterlongo, P., Pisanti, N., Boyer, F., Sagot, M.-F.: Lossless filter for finding long multiple approximate repetitions using a new data structure, the bi-factor array. In: Consens, M.P., Navarro, G. (eds.) SPIRE 2005. LNCS, vol. 3772, pp. 179–190. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  11. Schnattinger, T., Ohlebusch, E., Gog, S.: Bidirectional search in a string with wavelet trees. In: Amir, A., Parida, L. (eds.) CPM 2010. LNCS, vol. 6129, pp. 40–50. Springer, Heidelberg (2010)

    Chapter  Google Scholar 

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Author information

Authors and Affiliations

  1. Instituto Superior Técnico-Universidade Técnica de Lisboa (IST/UTL), Av. Rovisco Pais, 1049-001, Lisboa, Portugal

    Luís M. S. Russo

  2. INESC-ID, Knowledge Discovery and Bioinformatics Group, R. Alves Redol, 9, 1000-029, Lisbon, Portugal

    Luís M. S. Russo

  3. Lehrstuhl für Informatik II, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany

    German Tischler

Authors
  1. Luís M. S. Russo
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  2. German Tischler
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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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Russo, L.M.S., Tischler, G. (2011). Succinct Gapped Suffix Arrays. 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_28

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  • DOI: https://doi.org/10.1007/978-3-642-24583-1_28

  • 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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