Topological language for RNA

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【作者】 Fenix W. D. Huang  Christian M. Reidys 

【关键词】RNA Structure ARC CFG Secondary Structure Grammar 

【摘要】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 The code is written in C and compiled by Xcode.

【刊名】Mathematical biosciences