2692-4048ISSN (Online)
2770-0070ISSN (Print)
Volume 7 , Issue 2 , PP: 66-78, 2022 | Cite this article as | XML | Html | PDF | Full Length Article
Osama Maher 1
Doi: https://doi.org/10.54216/FPA.070201
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.
Computational Molecular Biology, Problem Aware Local Search, Harris Hawks Optimization, DNA Fragment Assembly Problem, Optimization
[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.
