Design of DNA Storage Coding with Enhanced Constraints

Traditional storage media have been gradually unable to meet the needs of data storage around the world, and one solution to this problem is DNA storage. However, it is easy to make errors in the subsequent sequencing reading process of DNA storage coding. To reduces error rates, a method to enhance...

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Bibliographic Details
Published in:Entropy (Basel, Switzerland) Vol. 24; no. 8; p. 1151
Main Authors: Li, Xiangjun, Zhou, Shihua, Zou, Lewang
Format: Journal Article
Language:English
Published: Switzerland MDPI AG 19.08.2022
MDPI
Subjects:
Algorithms
Aquila Optimizer
Codes
coding enhancement constraint
Computer storage devices
Data storage
DNA
DNA coding design
DNA sequencing
DNA storage
Error correction & detection
Error reduction
Gene sequencing
Genetic research
Hard disks
Hybridization
Lower bounds
Machine learning
Nucleotide sequencing
coding enhancement constraint
DNA coding design
DNA storage
Aquila Optimizer
ISSN:1099-4300, 1099-4300
Online Access:Get full text
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Summary:Traditional storage media have been gradually unable to meet the needs of data storage around the world, and one solution to this problem is DNA storage. However, it is easy to make errors in the subsequent sequencing reading process of DNA storage coding. To reduces error rates, a method to enhance the robustness of the DNA storage coding set is proposed. Firstly, to reduce the likelihood of secondary structure in DNA coding sets, a repeat tandem sequence constraint is proposed. An improved DTW distance constraint is proposed to address the issue that the traditional distance constraint cannot accurately evaluate non-specific hybridization between DNA sequences. Secondly, an algorithm that combines random opposition-based learning and eddy jump strategy with Aquila Optimizer (AO) is proposed in this paper, which is called ROEAO. Finally, the ROEAO algorithm is used to construct the coding sets with traditional constraints and enhanced constraints, respectively. The quality of the two coding sets is evaluated by the test of the number of issuing card structures and the temperature stability of melting; the data show that the coding set constructed with ROEAO under enhanced constraints can obtain a larger lower bound while improving the coding quality.
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ISSN:1099-4300
1099-4300
DOI:10.3390/e24081151