A complexity and approximation framework for the maximization scaffolding problem

Annie Chateau 1 Rodolphe Giroudeau 2
1 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
2 MAORE - Méthodes Algorithmes pour l'Ordonnancement et les Réseaux
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : We explore in this paper some complexity issues inspired by the contig scaffolding problem in bioinformatics. We focus on the following problem: given an undirected graph with no loop, and a perfect matching on this graph, find a set of cycles and paths covering every vertex of the graph, with edges alternatively in the matching and outside the matching, and satisfying a given constraint on the numbers of cycles and paths. We show that this problem is NP-complete, even in planar bipartite graphs. Moreover, we show that there is no subexponential-time algorithm for several related problems unless the Exponential-Time Hypothesis fails. Lastly, we also design two polynomial-time approximation algorithms for complete graphs.
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https://hal-lirmm.ccsd.cnrs.fr/lirmm-01219622
Contributor : Annie Chateau <>
Submitted on : Thursday, October 22, 2015 - 9:59:30 PM
Last modification on : Friday, April 12, 2019 - 10:18:09 AM

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Annie Chateau, Rodolphe Giroudeau. A complexity and approximation framework for the maximization scaffolding problem. Theoretical Computer Science, Elsevier, 2015, 595, pp.92-106. ⟨10.1016/j.tcs.2015.06.023⟩. ⟨lirmm-01219622⟩

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