title: Generation of RNA pseudoknot structures with topological genus filtration.
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.
authors.affiliation: Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark. Electronic address: fenixprotoss@gmail.com.
authors.forename: Fenix W D
authors.initials: FW
authors.lastname: Huang
authors.forename: Markus E
authors.initials: ME
authors.lastname: Nebel
authors.forename: Christian M
authors.initials: CM
authors.lastname: Reidys
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D055641:Mathematical Concepts; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA
keywords: Partition function; RNA pseudoknot structure; RNA secondary structure; Sampling; Topological genus; Topological surface