Thermodynamics of RNA structures by Wang-Landau sampling

Lou Feng 1, 2, * Peter Clote 3, 4
* 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 : Thermodynamics-based dynamic programming RNA secondary structure algorithms have been of immense importance in molecular biology, where applications range from the detection of novel selenoproteins using expressed sequence tag (EST) data, to the determination of microRNA genes and their targets. Dynamic programming algorithms have been developed to compute the minimum free energy secondary structure and partition function of a given RNA sequence, the minimum free-energy and partition function for the hybridization of two RNA molecules, etc. However, the applicability of dynamic programming methods depends on disallowing certain types of interactions (pseudoknots, zig-zags, etc.), as their inclusion renders structure prediction an nondeterministic polynomial time (NP)-complete problem. Nevertheless, such interactions have been observed in X-ray structures.
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Submitted on : Friday, December 3, 2010 - 8:49:55 AM
Last modification on : Wednesday, July 10, 2019 - 7:14:02 PM

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Lou Feng, Peter Clote. Thermodynamics of RNA structures by Wang-Landau sampling. Bioinformatics, Oxford University Press (OUP), 2010, 26, pp.278-286. ⟨10.1093/bioinformatics/btq218⟩. ⟨inria-00542620⟩

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