License: Creative Commons Attribution 4.0 International license (CC BY 4.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.WABI.2021.5
URN: urn:nbn:de:0030-drops-143586
URL: https://drops.dagstuhl.de/opus/volltexte/2021/14358/
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Boria, Nicolas ; Gourvès, Laurent ; Paschos, Vangelis Th. ; Monnot, Jérôme

The Maximum Duo-Preservation String Mapping Problem with Bounded Alphabet

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LIPIcs-WABI-2021-5.pdf (0.8 MB)


Abstract

Given two strings A and B such that B is a permutation of A, the max duo-preservation string mapping (MPSM) problem asks to find a mapping π between them so as to preserve a maximum number of duos. A duo is any pair of consecutive characters in a string and it is preserved by π if its two consecutive characters in A are mapped to same two consecutive characters in B. This problem has received a growing attention in recent years, partly as an alternative way to produce approximation algorithms for its minimization counterpart, min common string partition, a widely studied problem due its applications in comparative genomics. Considering this favored field of application with short alphabet, it is surprising that MPSM^𝓁, the variant of MPSM with bounded alphabet, has received so little attention, with a single yet impressive work that provides a 2.67-approximation achieved in O(n) [Brubach, 2018], where n = |A| = |B|. Our work focuses on MPSM^𝓁, and our main contribution is the demonstration that this problem admits a Polynomial Time Approximation Scheme (PTAS) when 𝓁 = O(1). We also provide an alternate, somewhat simpler, proof of NP-hardness for this problem compared with the NP-hardness proof presented in [Haitao Jiang et al., 2012].

BibTeX - Entry

@InProceedings{boria_et_al:LIPIcs.WABI.2021.5,
  author =	{Boria, Nicolas and Gourv\`{e}s, Laurent and Paschos, Vangelis Th. and Monnot, J\'{e}r\^{o}me},
  title =	{{The Maximum Duo-Preservation String Mapping Problem with Bounded Alphabet}},
  booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
  pages =	{5:1--5:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-200-6},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{201},
  editor =	{Carbone, Alessandra and El-Kebir, Mohammed},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/opus/volltexte/2021/14358},
  URN =		{urn:nbn:de:0030-drops-143586},
  doi =		{10.4230/LIPIcs.WABI.2021.5},
  annote =	{Keywords: Maximum-Duo Preservation String Mapping, Bounded alphabet, Polynomial Time Approximation Scheme}
}

Keywords: Maximum-Duo Preservation String Mapping, Bounded alphabet, Polynomial Time Approximation Scheme
Collection: 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
Issue Date: 2021
Date of publication: 22.07.2021


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