Contraction graphs for representation and analysis of RNA secondary structure

We introduce the contraction graph as a novel graphical representation of RNA secondary structure. A contraction operation - defined along base pairs, single stranded regions, and tertiary interactions - allows for representing RNA secondary structure at different levels of detail. Directionality of the graph and flow conservation of the contraction operation allow for explicit representation of the 5´ and 3´ ends of the molecule. Furthermore, existing representations such as tree and dual graphs are specific instances in this framework. We anticipate that this unified representation will facilitate automated motif finding and functional classification based on direct searches and comparisons of RNA secondary structure topology.