Versatile Succinct Representations of the Bidirectional Burrows-Wheeler Transform

  • Djamal Belazzougui
  • Fabio Cunial
  • Juha Kärkkäinen
  • Veli Mäkinen
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8125)


We describe succinct and compact representations of the bidirectional bwt of a string s ∈ Σ* which provide increasing navigation power and a number of space-time tradeoffs. One such representation allows to extend a substring of s by one character from the left and from the right in constant time, taking O(|s| log |Σ|) bits of space. We then match the functions supported by each representation to a number of algorithms that traverse the nodes of the suffix tree of s, exploiting connections between the bwt and the suffix-link tree. This results in near-linear time algorithms for many sequence analysis problems (e.g. maximal unique matches), for the first time in succinct space.


Maximal Repeat Wavelet Tree Short Read Alignment Bidirectional Search Absent Word 
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 2013

Authors and Affiliations

  • Djamal Belazzougui
    • 1
  • Fabio Cunial
    • 1
  • Juha Kärkkäinen
    • 1
  • Veli Mäkinen
    • 1
  1. 1.Helsinki Institute for Information Technology (HIIT), Department of Computer ScienceUniversity of HelsinkiFinland

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