RNA as a Permutation

TL;DR

This paper introduces a novel permutation-based method for clustering RNA secondary structures, aiming to improve classification and understanding of RNA development patterns.

Contribution

It presents a new permutation approach and a JAVA program for clustering RNA secondary structures, a method not previously used in this context.

Findings

Effective clustering of RNA secondary structures using permutation.

Potential to enhance understanding of RNA development patterns.

A simple yet powerful permutation-based classification method.

Abstract

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.