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DOI: 10.4230/LIPIcs.WABI.2021.5

The Maximum Duo-Preservation String Mapping Problem with Bounded Alphabet

Authors: Nicolas Boria, Laurent Gourvès, Vangelis Th. Paschos, and Jérôme Monnot

Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)

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].

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Nicolas Boria, Laurent Gourvès, Vangelis Th. Paschos, and Jérôme Monnot. The Maximum Duo-Preservation String Mapping Problem with Bounded Alphabet. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 5:1-5:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@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/entities/document/10.4230/LIPIcs.WABI.2021.5},
  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}
}

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The Maximum Duo-Preservation String Mapping Problem with Bounded Alphabet

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