Uniform and non-uniform random generation of RNA secondary structures with pseudoknots

Cédric Saule 1 Claire Wallon 1 Alain Denise 1, 2, 3, *
* Corresponding author
2 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 : We give an efficient algorithm to generate random RNA secondary structures with pseudoknots, either uniformly or non uniformly in a controllable fashion. Although we consider a restrictive class of pseudoknots, the class of {\em simple recursive pseudoknots}, it turns out that most of the known real RNA pseudoknotted secondary structures in the biological databases belong to this class.
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https://hal.inria.fr/inria-00543315
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Submitted on : Monday, December 6, 2010 - 1:11:41 PM
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Cédric Saule, Claire Wallon, Alain Denise. Uniform and non-uniform random generation of RNA secondary structures with pseudoknots. GASCOM, Sep 2010, Montreal, Canada. ⟨inria-00543315⟩

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