Efficient Algorithm for Circular Burrows-Wheeler Transform

  • Wing-Kai Hon
  • Tsung-Han Ku
  • Chen-Hua Lu
  • Rahul Shah
  • Sharma V. Thankachan
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7354)


Given a set \({\cal P}\) of d patterns, the circular dictionary matching problem is to index \({\cal P}\) such that for any online query text T, we can quickly locate the occurrences of any cyclic shift of any pattern of \({\cal P}\) within T efficiently. This problem can be applied on practical problems that arise in bioinformatics and computational geometry. Recently, Hon et al. (2011) applied a variant of the well-known Burrows-Wheeler transform, called circular Burrows-Wheeler transform (circular BWT) [Mantaci, Restivo, Rosone, and Sciortino, Theoretical Computer Science, 2007], and showed that this can be used to solve the circular dictionary matching problem efficiently. In this paper, we give the first construction algorithm for the circular BWT, which takes O(nlogn) time and requires O(nlogσ) bits working space, where n denotes the total length of the patterns in \({\cal P}\) and σ is the alphabet size.


Computational Geometry Vector Versus Relative Rank Construction Algorithm Cyclic Shift 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Wing-Kai Hon
    • 1
  • Tsung-Han Ku
    • 1
  • Chen-Hua Lu
    • 2
  • Rahul Shah
    • 3
  • Sharma V. Thankachan
    • 3
  1. 1.National Tsing Hua UniversityTaiwan
  2. 2.Academia SinicaTaiwan
  3. 3.Louisiana State UniversityUSA

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