Scaffolding Problems Revisited: Complexity, Approximation and Fixed Parameter Tractable Algorithms, and Some Special Cases

Mathias Weller 1, 2 Annie Chateau 3 Clément Dallard 4 Rodolphe Giroudeau 4
3 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
4 MAORE - Méthodes Algorithmes pour l'Ordonnancement et les Réseaux
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : This paper is devoted to new results about the scaffolding problem, an integral problem of genome inference in bioinformatics. The problem consists in finding a collection of disjoint cycles and paths covering a particular graph called the " scaffold graph ". We examine the difficulty and the approximability of the scaffolding problem in special classes of graphs, either close to trees, or very dense. We propose negative and positive results, exploring the frontier between difficulty and tractability of computing and/or approximating a solution to the problem. Also, we explore a new direction through related problems consisting in finding a family of edges having a strong effect on solution weight.
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Mathias Weller, Annie Chateau, Clément Dallard, Rodolphe Giroudeau. Scaffolding Problems Revisited: Complexity, Approximation and Fixed Parameter Tractable Algorithms, and Some Special Cases. Algorithmica, Springer Verlag, 2018, 80 (6), pp.1771 - 1803. ⟨10.1007/s00453-018-0405-x⟩. ⟨hal-01833303⟩

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