Mod/resc parsimony inference

  • Authors:

  • Igor Nor;Danny Hermelin;Sylvain Charlat;Jan Engelstadter;Max Reuter;Olivier Duron;Marie-France Sagot

  • Affiliations:

  • Université de Lyon, Lyon, CNRS, UMR and INRIA Grenoble, Rhône-Alpes, France;Max Planck Institute for Informatics, Saarbrücken, Germany;Université de Lyon, Lyon, CNRS, UMR;Institute of Integrative Biology, ETH Zurich, Switzerland;University College London, UK;Institute of Evolutionary Sciences, CNRS, University of Montpellier II, France;Université de Lyon, Lyon, CNRS, UMR and INRIA Grenoble, Rhône-Alpes, France

  • Venue:
  • CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
  • Year:
  • 2010

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Abstract

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 PARSIOMNY 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.