Graph-Based Analysis of RNA Secondary Structure Similarity Comparison

Author:

Yang Lina1,Liu Yang1ORCID,Hu Xiaochun2,Wang Patrick3,Li Xichun4,Wu Jun5

Affiliation:

1. Computer and Electronic Information, Guangxi University, Nanning 530004, China

2. School of Information and Statistics, Guangxi University of Finance and Economics, Nanning 530007, China

3. Computer and Information Science, Northeastern University, Boston 02115, USA

4. Guangxi Normal University for Nationalities, Chongzuo, China

5. School of Computer and Information Technology, Beijing Jiaotong University, Beijing 100044, China

Abstract

In organisms, ribonucleic acid (RNA) plays an essential role. Its function is being discovered more and more. Due to the conserved nature of RNA sequences, its function mainly depends on the RNA secondary structure. The discovery of an approximate relationship between two RNA secondary structures helps to understand their functional relationship better. It is an important and urgent task to explore structural similarities from the graphical representation of RNA secondary structures. In this paper, a novel graphical analysis method based on the triple vector curve representation of RNA secondary structures is proposed. A combinational method involving a discrete wavelet transform (DWT) and fractal dimension with sliding window is introduced to analyze and compare the graphs derived from feature extraction; after that, the distance matrix is generated. Then, the distance matrix is analyzed by clustering and visualized as a clustering tree. RNA virus and noncoding RNA datasets are applied to perform experiments and analyze the clustering tree. The results show that the proposed method yields more accurate results in the comparison of RNA secondary structures.

Funder

National Natural Science Foundation of China

Publisher

Hindawi Limited

Subject

Multidisciplinary,General Computer Science

Reference65 articles.

1. Popularização da Ciência: Desmistificando o Dogma Central da Biologia Molecular

2. Accurate prediction of genome-wide rna secondary structure profile based on extreme gradient boosting.;Y. Ke,2019

3. Predicting RNA secondary structure via adaptive deep recurrent neural networks with energy-based filter

4. Mapping RNA–capsid interactions and RNA secondary structure within virus particles using next-generation sequencing

5. Comparison of pseudoknotted RNA secondary structures by topological centroid identification and tree edit distance;F. Wang;Journal of Computational Biology,2020

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