Efficient algorithm for circular burrows-wheeler transform

Authors:
Wing-Kai Hon;Tsung-Han Ku;Chen-Hua Lu;Rahul Shah;Sharma V. Thankachan
Affiliations:
National Tsing Hua University, Taiwan;National Tsing Hua University, Taiwan;Academia Sinica, Taiwan;Louisiana State University;Louisiana State University
Venue:
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
Year:
2012

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Abstract

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.