A 2D graphical representation of RNA secondary structures and the analysis of similarity/dissimilarity based on it

A 2D graphical representation of RNA secondary structures is given in terms of classifications of bases of nucleic acids. The novel graphical representation can completely avoid loss of information associated with crossing and overlapping of the corresponding curve. Afterwards, we make quantitative analysis for a set of RNA secondary structures at the 3′-terminus of different viruses based on this graphical representation. The examination of similarities/dissimilarities illustrates the utility of the approach.