An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures.

ABSTRACT: Exploring novel RNA topologies is imperative for understanding RNA structure and pursuing its design. Our RNA-As-Graphs (RAG) approach exploits graph theory tools and uses coarse-grained tree and dual graphs to represent RNA helices and loops by vertices and edges. Only dual graphs represent pseudoknotted RNAs fully. Here we develop a dual graph enumeration algorithm to generate an expanded library of dual graph topologies for 2-9 vertices, and extend our dual graph partitioning algorithm to identify all possible RNA subgraphs. Our enumeration algorithm connects smaller-vertex graphs, using all possible edge combinations, to build larger-vertex graphs and retain all non-isomorphic graph topologies, thereby more than doubling the size of our prior library to a total of 110,667 dual graph to

SUBMITTER: Jain S 

PROVIDER: S-EPMC6612455 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature