Analysis of similarity of RNA secondary structures based on a 2D graphical representation

We introduce a 2D graphical representation of RNA secondary structures, which has an important advantage over the existing graphical representations of RNA in being very compact. Then we transform the 2D graph into a numerical characterization that will facilitate quantitative comparisons of RNA secondary structures. The examination of similarities/dissimilarities of a set of RNA secondary structures at the 3′-terminus of nine different viruses illustrates the utility of the approach.