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