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New Approach in Genetic Algorithm for RNA Secondary Structure Prediction

Binh Doan Duy 1, Minh Tuan Pham 2, Long Dang Duc 3, and Long Dang Duc 4
1. Faculty of Information Technology, Danang University of Science and Education, the University of Danang, Vietnam
2. IT Faculty, Danang University of Science and Technology, the University of Danang, Vietnam
3. VN-UK Institute for Research & Executive Education, the University of Danang, Vietnam
4. Learning and Research Center, Quang Binh University, Vietnam

Abstract—RNA secondary structure problem is one of the most important fields in computational molecular biology. Ribonucleic Acid (RNA) has important structural and functional roles in the cell and plays roles in many stages of protein synthesis. The structure of RNA largely determines its function. Many methods can be used to predict the secondary structure of an RNA molecule. One of the methods is the dynamic programming approach. However, the dynamic programming approach usually takes too much time. Genetic algorithm is an evolutionary approach for solving space layout and optimization problems. Due to some drawbacks in genetic algorithm, several modifications are performed on this algorithm. When the advantages of GA are combined with advantages of another algorithm then this approach is called Hybrid Genetic Algorithm. In this paper we introduce a hybrid Genetic Algorithm with Fuzzy Logic. From this hybrid algorithm we apply the problem of predicting the secondary structure of Ribonucleic Acid. Problem predicted secondary structure that we mentioned methods based on thermodynamics, to find secondary structure with minimum energy. With the results of the algorithms found by the hybrid algorithm we introduce, we hope to contribute to the molecular biology data warehouse for molecular biology research. It also introduces a new approach to genetic algorithms.
Index Terms—genetic algorithm, dynamic programming algorithms, minimum free energy, fuzzy logic, RNA secondary structure, computational biology

Cite: Binh Doan Duy, Minh Tuan Pham, Long Dang Duc, and Hoan Dau Manh, "New Approach in Genetic Algorithm for RNA Secondary Structure Prediction," Journal of Advances in Information Technology, Vol. 11, No. 4, pp. 249-258, November 2020. doi: 10.12720/jait.11.4.249-258

Copyright © 2020 by the authors. This is an open access article distributed under the Creative Commons Attribution License (CC BY-NC-ND 4.0), which permits use, distribution and reproduction in any medium, provided that the article is properly cited, the use is non-commercial and no modifications or adaptations are made.