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arXiv · 1304.7397

Uniform generation of RNA pseudoknot structures with genus filtration

Fenix W. D. Huang·Markus E. Nebel·Christian M. Reidys
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Abstract

In this paper we present a sampling framework for RNA structures of fixed topological genus. We introduce a novel, linear time, uniform sampling algorithm for RNA structures of fixed topological genus $g$, for arbitrary $g>0$. Furthermore we develop a linear time sampling algorithm for RNA structures of fixed topological genus $g$ that are weighted by a simplified, loop-based energy functional. For this process the partition function of the energy functional has to be computed once, which has $O(n^2)$ time complexity.

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Fenix W. D. Huang, Markus E. Nebel, Christian M. Reidys. 2013-04-27. Uniform generation of RNA pseudoknot structures with genus filtration. https://arxiv.org/abs/1304.7397

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