Similarity of RNA secondary structures

In this article, we propose a relatively similar measure to compare RNA secondary structures. We first transform an RNA secondary structure into a special sequence representation. Then, on the basis of symbolic sequence complexity. we obtain the relative distance of RNA secondary structures. The examination of similarities/dissimilarities of a set of RNA secondary structures at the 3'-terminus of different viruses illustrates the utility of the approach. (C) 2006 Wiley Periodicals, Inc.