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.2017.11
URN: urn:nbn:de:0030-drops-73436
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2017/7343/
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Komusiewicz, Christian ; de Oliveira Oliveira, Mateus ; Zehavi, Meirav

Revisiting the Parameterized Complexity of Maximum-Duo Preservation String Mapping

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Abstract

In the Maximum-Duo Preservation String Mapping (Max-Duo PSM) problem, the input consists of two related strings A and B of length n and a nonnegative integer k. The objective is to determine whether there exists a mapping m from the set of positions of A to the set of positions of B that maps only to positions with the same character and preserves at least k duos, which are pairs of adjacent positions. We develop a randomized algorithm that solves Max-Duo PSM in time 4^k * n^{O(1)}, and a deterministic algorithm that solves this problem in time 6.855^k * n^{O(1)}. The previous best known (deterministic) algorithm for this problem has running time (8e)^{2k+o(k)} * n^{O(1)} [Beretta et al., Theor. Comput. Sci. 2016]. We also show that Max-Duo PSM admits a problem kernel of size O(k^3), improving upon the previous best known problem kernel of size O(k^6).

BibTeX - Entry

@InProceedings{komusiewicz_et_al:LIPIcs:2017:7343,
  author =	{Christian Komusiewicz and Mateus de Oliveira Oliveira and Meirav Zehavi},
  title =	{{Revisiting the Parameterized Complexity of Maximum-Duo Preservation String Mapping}},
  booktitle =	{28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017)},
  pages =	{11:1--11:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-039-2},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{78},
  editor =	{Juha K{\"a}rkk{\"a}inen and Jakub Radoszewski and Wojciech Rytter},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2017/7343},
  URN =		{urn:nbn:de:0030-drops-73436},
  doi =		{10.4230/LIPIcs.CPM.2017.11},
  annote =	{Keywords: comparative genomics, parameterized complexity, kernelization}
}

Keywords: comparative genomics, parameterized complexity, kernelization
Collection: 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017)
Issue Date: 2017
Date of publication: 30.06.2017

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