Approximating the 2-interval pattern problem

Authors:
Maxime Crochemore;Danny Hermelin;Gad M. Landau;Dror Rawitz;Stéphane Vialette
Affiliations:
Institut Gaspard-Monge, Université de Marne-la-Vallée, France and Department of Computer Science, Kings Collage, London, UK;Department of Computer Science, University of Haifa, Israel;Department of Computer Science, University of Haifa, Israel and Department of Computer and Information Science, Polytechnic University, NY, USA;Caesarea Rothschild Institute (CRI), University of Haifa, Israel;Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud, France
Venue:
Theoretical Computer Science
Year:
2008

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Abstract

We address the issue of approximating the 2-Interval Pattern problem over its various models and restrictions. This problem, motivated by RNA secondary structure prediction, asks to find a maximum cardinality subset of a 2-interval set with respect to some prespecified geometric constraints. We present several constant factor approximation algorithms whose performance guarantee depends on the different possible restrictions imposed on the input 2-interval set. In addition, we show that our results extend to the weighted variant of the problem.