Volume 7 • Issue 2 • PP: 66-78 • 2022
An Intelligent Optimization Model for Fragment Assembly Problem
Open Access & Copyright
© 2022 The Author(s). Published by ASPG. This article is licensed under the Creative Commons Attribution 4.0 International License (CC BY 4.0).
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problem as it requires rebuilding the original sequence of DNA from a massive number of fragments. This paper introduces an efficient hybridization between Harris Hawks Optimization (HHO) and Problem Aware Local Search (PALS) to be utilized in solving DNA Fragment Assembly Problem (FAP). The efficiency of the proposed hybrid algor In computational molecular biology, the sequencing of Deoxyribonucleic Acid (DNA) is a very challenging ithm (PHHO) is compared with the original PALS, Firefly Algorithm (FA), Genetic Algorithm (GA), Artificial Bee Colony (ABC), and GAG50. The experimental results show the efficiency of the proposed algorithm compared to other approaches.
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References
[1] Knetsch, C. W., van der Veer, E. M., Henkel, C., & Taschner, P. (2019). DNA Sequencing. In Molecular Diagnostics (pp. 339-360). Springer, Singapore.
[2] Huang, X., & Madan, A. (1999). CAP3: A DNA sequence assembly program. Genome research, 9(9), 868- 877.
[3] Green, P. (2009). Phrap, version 1.090518; 2009.
[4] Myers, E. W., Sutton, G. G., Delcher, A. L., Dew, I. M., Fasulo, D. P., Flanigan, M. J., ... & Anson, E. L. (2000). A whole-genome assembly of Drosophila. Science, 287(5461), 2196-2204.
[5] Sutton, G. G., White, O., Adams, M. D., & Kerlavage, A. R. (1995). TIGR Assembler: A new tool for assembling large shotgun sequencing projects. Genome Science and Technology, 1(1), 9-19.
[6] Chen, T., & Skiena, S. S. (2000). A case study in genome-level fragment assembly. Bioinformatics, 16(6), 494-500.
[7] Firoz, J. S., Rahman, M. S., & Saha, T. K. (2012, July). Bee algorithms for solving DNA fragment assembly problem with noisy and noiseless data. In Proceedings of the 14th annual conference on Genetic and evolutionary computation ,201-208.
[8] Minetti, G., Alba, E., & Luque, G. (2008). Seeding strategies and recombination operators for solving the DNA fragment assembly problem. Information Processing Letters, 108(3), 94-100.
[9] Ezzeddine, A. B., Kasala, S., & Navrat, P. (2014). Applying the firefly approach to the DNA fragments assembly problem. In Annales Univ. Sci. Budapest., Sect. Comp, 69-81.
[10] Allaoui, M., Ahiod, B., & El Yafrani, M. (2018). A hybrid crow search algorithm for solving the DNA fragment assembly problem. Expert Systems with Applications, 102, 44-56.
[11] Minetti, G., & Alba, E. (2010, July). Metaheuristic assemblers of DNA strands: Noiseless and noisy cases. In IEEE Congress on Evolutionary Computation (pp. 1-8). IEEE.
[12] Earl, D., Bradnam, K., John, J. S., Darling, A., Lin, D., Fass, J., ... & Nguyen, N. (2011). Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome research, 21(12), 2224-2241.
[13] Heidari, A. A., Mirjalili, S., Faris, H., Aljarah, I., Mafarja, M., & Chen, H. (2019). Harris hawks optimization: Algorithm and applications. Future generation computer systems, 97, 849-872.
[14] Abdel-Basset, M., Abdel-Fatah, L., & Sangaiah, A. K. (2018). Metaheuristic algorithms: A comprehensive review. In Computational intelligence for multimedia big data on the cloud with engineering applications (pp. 185-231). Academic Press.
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