A Characteristic Sequences and Normalized Euclidean Distance Based Method for RNA Secondary Structures Comparison

In this paper, an approach for the comparison of RNA secondary structures (not allowing for pseudoknots) is developed. To measure the difference of different secondary structures, a normalized Euclidean distance is employed based on so called characteristic sequences of RNA secondary structures, which avoids the influence of the difference in length of secondary structures under consideration. The application of our method to a set of real data shows the effectiveness of our proposed method.