Uniform generation of RNA pseudoknot structures with genus filtration

Autor:	Huang, Fenix W. D., Nebel, Markus E., Reidys, Christian M.
Rok vydání:	2013
Předmět:	Computer Science - Computational Engineering Finance and Science Mathematics - Combinatorics Quantitative Biology - Biomolecules 05C85
Druh dokumentu:	Working Paper
Popis:	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. Comment: 11 figures, 25 pages
Databáze:	arXiv
Externí odkaz:	http://arxiv.org/abs/1304.7397 Zobrazit plný text záznamu View this record from Arxiv