Generation of RNA pseudoknot structures with topological genus filtration |
| |
Authors: | Fenix W.D. Huang Markus E. Nebel Christian M. Reidys |
| |
Affiliation: | 1. Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark;2. Department of Computer Science, University of Kaiserslautern, Germany |
| |
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(n2) time complexity. |
| |
Keywords: | RNA secondary structure RNA pseudoknot structure Topological surface Topological genus Partition function Sampling |
本文献已被 ScienceDirect 等数据库收录! |
|