Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility - Inria - Institut national de recherche en sciences et technologies du numérique Access content directly
Journal Articles Algorithms for Molecular Biology Year : 2020

Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility

Abstract

Cytoplasmic incompatibility (CI) relates to the manipulation by the parasite Wolbachia of its host reproduction. Despite its widespread occurrence, the molecular basis of CI remains unclear and theoretical models have been proposed to understand the phenomenon. We consider in this paper the quantitative Lock-Key model which currently represents a good hypothesis that is consistent with the data available. CI is in this case modelled as the problem of covering the edges of a bipartite graph with the minimum number of chain subgraphs. This problem is already known to be NP-hard, and we provide an exponential algorithm with a non trivial complexity. It is frequent that depending on the dataset, there may be many optimal solutions which can be biologically quite different among them. To rely on a single optimal solution may therefore be problematic. To this purpose, we address the problem of enumerating (listing) all minimal chain subgraph covers of a bipartite graph and show that it can be solved in quasi-polynomial time. Interestingly, in order to solve the above problems, we considered also the problem of enumerating all the maximal chain subgraphs of a bipartite graph and improved on the current results in the literature for the latter. Finally, to demonstrate the usefulness of our methods we show an application on a real dataset.
Fichier principal
Vignette du fichier
s13015-020-00174.pdf (3.67 Mo) Télécharger le fichier
Origin : Publisher files allowed on an open archive
Loading...

Dates and versions

hal-02917569 , version 1 (19-08-2020)

Identifiers

Cite

Tiziana Calamoneri, Mattia Gastaldello, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri. Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility. Algorithms for Molecular Biology, 2020, pp.1-16. ⟨10.1186/s13015-020-00174-1⟩. ⟨hal-02917569⟩
70 View
63 Download

Altmetric

Share

Gmail Facebook X LinkedIn More