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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| Abstract | 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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| AbstractList | 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.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. 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. |
| Audience | Academic |
| Author | Li, Xiangjun Zou, Lewang Zhou, Shihua |
| AuthorAffiliation | Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, Dalian University, Dalian 116622, China |
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| Keywords | coding enhancement constraint DNA coding design DNA storage Aquila Optimizer |
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| SubjectTerms | 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 |
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| Title | Design of DNA Storage Coding with Enhanced Constraints |
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