A class of 2D graphical representations of RNA secondary structures and the analysis of similarity based on them.

Based on the concepts of cell and system of graphical representation, a class of 2D graphical representations of RNA secondary structures are given in terms of classifications of bases of nucleic acids. The representations can completely avoid loss of information associated with crossing and overlapping of the corresponding curve. As an application, we make quantitative comparisons for a set of RNA secondary structures at the 3'-terminus of different viruses based on the graphical representations. The examination of similarities/dissimilarities illustrates the utility of the approach. (c) 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1339-1346, 2005.