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Compressed Text Indexing with Wildcards

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Book cover 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

Let \(T=T_1\phi^{k_1}T_2\phi^{k_2}\cdots\phi^{k_d}T_{d+1}\) be a text of total length n, where characters of each T i are chosen from an alphabet Σ of size σ, and φ denotes a wildcard symbol. The text indexing with wildcards problem is to index T such that when we are given a query pattern P, we can locate the occurrences of P in T efficiently. This problem has been applied in indexing genomic sequences that contain single-nucleotide polymorphisms (SNP) because SNP can be modeled as wildcards. Recently Tam et al. (2009) and Thachuk (2011) have proposed succinct indexes for this problem. In this paper, we present the first compressed index for this problem, which takes only nH h  + o(n logσ) + O(d logn) bits space, where H h is the hth-order empirical entropy (h = o(log σ n)) of T.

This work is supported in part by Taiwan NSC Grant 99-2221-E-007-123 (W. Hon) and US NSF Grant CCF–1017623 (R. Shah).

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Author information

Authors and Affiliations

  1. National Tsing Hua University, Taiwan

    Wing-Kai Hon & Tsung-Han Ku

  2. Louisiana State University, USA

    Rahul Shah & Sharma V. Thankachan

  3. The University of Kansas, USA

    Jeffrey Scott Vitter

Authors
  1. Wing-Kai Hon
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  2. Tsung-Han Ku
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  3. Rahul Shah
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  4. Sharma V. Thankachan
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  5. Jeffrey Scott Vitter
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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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Hon, WK., Ku, TH., Shah, R., Thankachan, S.V., Vitter, J.S. (2011). Compressed Text Indexing with Wildcards. 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_26

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  • DOI: https://doi.org/10.1007/978-3-642-24583-1_26

  • 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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