Comparison Of RNA Secondary Structure Using Discrete Wavelet Transform And Fractal Dimension

As the role of RNA molecules was discovered more and more, the similarity between RNA sequences was studied widely. However, because RNA has a conserved secondary structure rather than a primary structure, it is important to consider structural information in RNA comparisons. In this paper, an RNA secondary structure comparison method based on fractal dimension and wavelet transform is proposed. First, the secondary structure of RNA was represented as TV-curve. Next, based on wavelet transform, the windowed fractal dimension is applied to calculate the similarity between sequences. RNA sequences from the RFAM database were selected for the experiment, and the results obtained were closer to the standard MEGA software compared with Li's algorithm, with lower time complexity.

1. Introduction

In organisms, there are mainly three different RNA molecules play an important role in the process of gene expression. They are messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA). Various RNAs have diverse functionalities. For example, Messenger RNA (mRNA) carries information from DNA by transcription, guides the synthesis of certain proteins [1]. Transfer RNA (tRNA) molecules to deliver satisfactory amino acids to the ribosome [2]. RNA contains the genetic material of virus, such as HIV. Of course, some noncoding RNAs are transcribed from genome, not involved in protein synthesis, and they can perform their biological functions at the RNA level.