RNA as a Permutation

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.