An Intelligent Optimization Algorithm for Constructing a DNA Storage Code: NOL-HHO
Open Access
- 22 March 2020
- journal article
- research article
- Published by MDPI AG in International Journal of Molecular Sciences
- Vol. 21 (6), 2191
- https://doi.org/10.3390/ijms21062191
Abstract
The high density, large capacity, and long-term stability of DNA molecules make them an emerging storage medium that is especially suitable for the long-term storage of large datasets. The DNA sequences used in storage need to consider relevant constraints to avoid nonspecific hybridization reactions, such as the No-runlength constraint, GC-content, and the Hamming distance. In this work, a new nonlinear control parameter strategy and a random opposition-based learning strategy were used to improve the Harris hawks optimization algorithm (for the improved algorithm NOL-HHO) in order to prevent it from falling into local optima. Experimental testing was performed on 23 widely used benchmark functions, and the proposed algorithm was used to obtain better coding lower bounds for DNA storage. The results show that our algorithm can better maintain a smooth transition between exploration and exploitation and has stronger global exploration capabilities as compared with other algorithms. At the same time, the improvement of the lower bound directly affects the storage capacity and code rate, which promotes the further development of DNA storage technology.Funding Information
- The National Natural Science Foundation of China (61425002, 61751203, 61772100, 61972266, 61802040, 61672121, 61572093)
- Natural Science Foundation of Liaoning Province (20180551241, 2019-ZD-0567)
- Scientific Research Fund of Liaoning Provincial Education Department (JYT19051)
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