Computing the Burrows-Wheeler transform of a string and its reverse in parallel

Authors:
Enno Ohlebusch;Timo Beller;Mohamed I. Abouelhoda
Affiliations:
Institute of Theoretical Computer Science, University of Ulm, 89069 Ulm, Germany;Institute of Theoretical Computer Science, University of Ulm, 89069 Ulm, Germany;Center for Informatics Sciences, Nile University, Giza, Egypt and Faculty of Engineering, Cairo University, Giza, Egypt
Venue:
Journal of Discrete Algorithms
Year:
2014

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Abstract

The contribution of this article is twofold. First, we provide new theoretical insights into the relationship between a string and its reverse: If the Burrows-Wheeler transform (BWT) of a string has been computed by sorting its suffixes, then the BWT, the suffix array, and the longest common prefix array of the reverse string can be derived from it without suffix sorting. Furthermore, we show that the longest common prefix arrays of a string and its reverse are permutations of each other. Second, we provide a parallel algorithm that, given the BWT of a string, computes the BWT of its reverse much faster than all known (parallel) suffix sorting algorithms. Some bioinformatics applications will benefit from this.