  RNA secondary structure prediction and classification are two important
problems in the field of RNA biology. Here, we propose a new permutation based
approach to create logical non-disjoint clusters of different secondary
structures of a single class or type. Many different types of techniques exist
to classify RNA secondary structure data but none of them have ever used
permutation based approach which is very simple and yet powerful. We have
written a small JAVA program to generate permutation, apply our algorithm on
those permutations and analyze the data and create different logical clusters.
We believe that these clusters can be utilized to untangle the mystery of RNA
secondary structure and analyze the development patterns of unknown RNA.
