Counting RNA pseudoknotted structures

Cédric Saule 1, 2 Mireille Regnier 1, 3, * Jean-Marc Steyaert 1, 3 Alain Denise 1, 2
* Corresponding author
1 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
Abstract : In 2004, Condon and coauthors gave a hierarchical classification of exact RNA structure prediction algorithms according to the generality of structure classes that they handle. We complete this classification by adding two recent prediction algo- rithms. More importantly, we precisely quantify the hierarchy by giving closed or asymptotic formulas for the theoretical number of structures of given size n in all the classes but one. This allows to assess the tradeoff between the expressiveness and the computational complexity of RNA structure prediction algorithms.
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Cédric Saule, Mireille Regnier, Jean-Marc Steyaert, Alain Denise. Counting RNA pseudoknotted structures. Journal of Computational Biology, Mary Ann Liebert, 2011, 18 (10), pp.1339-1351. ⟨10.1089/cmb.2010.0086⟩. ⟨inria-00537117⟩

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