License: Creative Commons Attribution 3.0 Unported license (CC BY 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.CPM.2019.24
URN: urn:nbn:de:0030-drops-104955
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2019/10495/
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Cazaux, Bastien ; Rivals, Eric

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

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LIPIcs-CPM-2019-24.pdf (0.7 MB)

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.

BibTeX - Entry

@InProceedings{cazaux_et_al:LIPIcs:2019:10495,
  author =	{Bastien Cazaux and Eric Rivals},
  title =	{{Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding}},
  booktitle =	{30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)},
  pages =	{24:1--24:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-103-0},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{128},
  editor =	{Nadia Pisanti and Solon P. Pissis},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2019/10495},
  URN =		{urn:nbn:de:0030-drops-104955},
  doi =		{10.4230/LIPIcs.CPM.2019.24},
  annote =	{Keywords: Data Structure, Algorithm, Aho-Corasick Tree, compression, RLE}
}

Keywords: Data Structure, Algorithm, Aho-Corasick Tree, compression, RLE
Collection: 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)
Issue Date: 2019
Date of publication: 06.06.2019
Supplementary Material: Source code at: https://framagit.org/bcazaux/compressbwt

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