Topological language for RNA. In this paper we introduce a novel, context-free grammar, RNAFeatures*, capable of generating any RNA structure including pseudoknot structures (pk-structure). We represent pk-structures as orientable fatgraphs, which naturally leads to a filtration by their topological genus. Within this framework, RNA secondary structures correspond to pk-structures of genus zero. RNAFeatures* acts on formal, arc-labeled RNA secondary structures, called λ-structures. λ-structures correspond one-to-one to pk-structures together with some additional information. This information consists of the specific rearrangement of the backbone, by which a pk-structure can be made cross-free. RNAFeatures* is an extension of the grammar for secondary structures and employs an enhancement by labelings of the symbols as well as the production rules. We discuss how to use RNAFeatures* to obtain a stochastic context-free grammar for pk-structures, using data of RNA sequences and structures. The induced grammar facilitates fast Boltzmann sampling and statistical analysis. As a first application, we present an O(nlog (n)) runtime algorithm which samples pk-structures based on ninety tRNA sequences and structures from the Nucleic Acid Database (NDB). Availability: the source code for simulation results is available at http://staff.vbi.vt.edu/fenixh/TPstructure.zip. The code is written in C and compiled by Xcode.
Keywords for this software
References in zbMATH (referenced in 4 articles , 1 standard article )
Showing results 1 to 4 of 4.
- Bura, Andrei C.; He, Qijun; Reidys, Christian M.: Loop homology of bi-secondary structures (2021)
- Huang, Fenix; Reidys, Christian; Rezazadegan, Reza: Fatgraph models of RNA structure (2017)
- Li, Thomas J. X.; Reidys, Christian M.: Statistics of topological RNA structures (2017)
- Huang, Fenix W. D.; Reidys, Christian M.: Topological language for RNA (2016)