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arXiv · 1805.10070

Strong link between BWT and XBW via Aho-Corasick automaton and applications to Run-Length Encoding

Bastien Cazaux·Eric Rivals
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Abstract

The boom of genomic sequencing makes compression of set of sequences inescapable. This underlies the need for multi-string indexing data structures that helps compressing the data. The most prominent example of such data structures is the Burrows-Wheeler Transform (BWT), a reversible permutation of a text that improves its compressibility. A similar data structure, the eXtended Burrows-Wheeler Transform (XBW), is able to index a tree labelled with alphabet symbols. A link between a multi-string BWT and the Aho-Corasick automaton has already been found and led to a way to build a XBW from a multi-string BWT. We exhibit a stronger link between a multi-string BWT and a XBW by using the order of the concatenation in the multi-string. This bijective link has several applications: first, it allows to build one data structure from the other; second, it enables one to compute an ordering of the input strings that optimises a Run-Length measure (i.e., the compressibility) of the BWT or of the XBW.

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Bastien Cazaux, Eric Rivals. 2018-05-25. Strong link between BWT and XBW via Aho-Corasick automaton and applications to Run-Length Encoding. https://doi.org/10.4230/lipics.cpm.2019.24

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