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- Source :
- Algorithms for Molecular Biology.
-
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.
- Subjects :
- 0106 biological sciences
Record locking
Basis (linear algebra)
Computer science
Applied Mathematics
0102 computer and information sciences
01 natural sciences
Exponential function
010601 ecology
Computational Theory and Mathematics
Chain (algebraic topology)
010201 computation theory & mathematics
Structural Biology
Bipartite graph
Key (cryptography)
Interval order
Molecular Biology
Algorithm
Cytoplasmic incompatibility
Subjects
Details
- ISSN :
- 17487188
- Database :
- OpenAIRE
- Journal :
- Algorithms for Molecular Biology
- Accession number :
- edsair.doi...........7b49157a1a0e38732e92a797a9b08fd1