Revisiting the parameterized complexity of maximum-duo preservation string mapping

Christian Komusiewicz, Mateus De Oliveira Oliveira, Meirav Zehavi

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

2 Scopus citations

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 MAXDUO PSM in time 4k · nO(1) a deterministic algorithm that solves this problem in time 6.855k · nO(1). The previous best known (deterministic) algorithm for this problem has running time (8e)2k+o(k) · nO(1) [Beretta et al., Theor. Comput. Sci. 2016]. We also show that MAX-DUO PSM admits a problem kernel of size O(k3), improving upon the previous best known problem kernel of size O(k6).

Original languageEnglish
Title of host publication28th Annual Symposium on Combinatorial Pattern Matching, CPM 2017
EditorsJakub Radoszewski, Juha Karkkainen, Jakub Radoszewski, Wojciech Rytter
PublisherSchloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
ISBN (Electronic)9783959770392
DOIs
StatePublished - 1 Jul 2017
Externally publishedYes
Event28th Annual Symposium on Combinatorial Pattern Matching, CPM 2017 - Warsaw, Poland
Duration: 4 Jul 20176 Jul 2017

Publication series

NameLeibniz International Proceedings in Informatics, LIPIcs
Volume78
ISSN (Print)1868-8969

Conference

Conference28th Annual Symposium on Combinatorial Pattern Matching, CPM 2017
Country/TerritoryPoland
CityWarsaw
Period4/07/176/07/17

Keywords

  • Comparative genomics
  • Kernelization
  • Parameterized complexity

ASJC Scopus subject areas

  • Software

Fingerprint

Dive into the research topics of 'Revisiting the parameterized complexity of maximum-duo preservation string mapping'. Together they form a unique fingerprint.

Cite this