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Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding

Authors Bastien Cazaux , Eric Rivals

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ACM Subject Classification
  • Mathematics of computing → Discrete mathematics
  • Theory of computation → Randomness, geometry and discrete structures
  • Theory of computation → Data structures and algorithms for data management
Keywords
  • Data Structure
  • Algorithm
  • Aho-Corasick Tree
  • compression
  • RLE

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Abstract

The boom of genomic sequencing makes compression of sets 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 one 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.

Cite As Get BibTex

Bastien Cazaux and Eric Rivals. Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding. In 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 128, pp. 24:1-24:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019) https://doi.org/10.4230/LIPIcs.CPM.2019.24

Author Details

Bastien Cazaux
  • Department of Computer Science, University of Helsinki, Finland
  • L.I.R.M.M., CNRS, Université Montpellier, France
Eric Rivals
  • L.I.R.M.M., CNRS, Université Montpellier, France

Funding

Support from the Institut de Biologie Computationnelle (ANR-11-BINF-0002).
  • Rivals, Eric: thanks the GEM Flagship project funded from Labex NUMEV (ANR-10-LABX-0020).

Supplementary Materials

References

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