Compressed Text Indexing with Wildcards

  • Wing-Kai Hon
  • Tsung-Han Ku
  • Rahul Shah
  • Sharma V. Thankachan
  • Jeffrey Scott Vitter
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7024)


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.


Locus Node Query Range Query Time Storage Scheme Query Pattern 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Wing-Kai Hon
    • 1
  • Tsung-Han Ku
    • 1
  • Rahul Shah
    • 2
  • Sharma V. Thankachan
    • 2
  • Jeffrey Scott Vitter
    • 3
  1. 1.National Tsing Hua UniversityTaiwan
  2. 2.Louisiana State UniversityUSA
  3. 3.The University of KansasUSA

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