Mod/Resc Parsimony Inference

Igor Nor (1, 2) , Danny Hermelin (3) , Sylvain Charlat (4) , Jan Engelstadter (5) , Max Reuter (6) , Olivier Duron (7) , Marie-France Sagot (1, 2)

1 Baobab
2 BAMBOO - An algorithmic view on genomes, cells, and environments
3 Department of Computer Science [Haifa]
4 Génétique et évolution des interactions hôtes-parasites
5 Department of Integrative Biology [Zurich]
6 UCL - University College of London [London]
7 UMR ISEM - Institut des Sciences de l'Evolution de Montpellier

We address in this paper a new computational biology problem that aims at understanding a mechanism that could potentially be used to genetically manipulate natural insect populations infected by inherited, intra-cellular parasitic bacteria. In this problem, that we denote by Mod/Resc Parsimony Inference, we are given a boolean matrix and the goal is to find two other boolean matrices with a minimum number of columns such that an appropriately defined operation on these matrices gives back the input. We show that this is formally equivalent to the Bipartite Biclique Edge Cover problem and derive some complexity results for our problem using this equivalence. We provide a new, fixed-parameter tractability approach for solving both that slightly improves upon a previously published algorithm for the Bipartite Biclique Edge Cover. Finally, we present experimental results where we applied some of our techniques to a real-life data set.

Domaines: Algorithme et structure de données [cs.DS]; Bio-Informatique, Biologie Systémique [q-bio.QM]; Bio-informatique [q-bio.QM]

Igor Nor, Danny Hermelin, Sylvain Charlat, Jan Engelstadter, Max Reuter, et al.. Mod/Resc Parsimony Inference. Combinatorial Pattern Matching, Jun 2010, New York, United States. pp.202--213, ⟨10.1007/978-3-642-13509-5_19⟩. ⟨hal-00681830⟩