Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors
With ultra-high density and preservation longevity, deoxyribonucleic acid (DNA)-based data storage is becoming an emerging storage technology. Limited by the current biochemical techniques, data might be corrupted during the processes of DNA data storage. A hybrid coding architecture consisting of m...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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IEEE
2019-01-01
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| Series: | IEEE Access |
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| Online Access: | https://ieeexplore.ieee.org/document/8746106/ |
| _version_ | 1818620847088205824 |
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| author | Li Deng Yixin Wang MD. Noor-A-Rahim Yong Liang Guan Zhiping Shi Erry Gunawan Chueh Loo Poh |
| author_facet | Li Deng Yixin Wang MD. Noor-A-Rahim Yong Liang Guan Zhiping Shi Erry Gunawan Chueh Loo Poh |
| author_sort | Li Deng |
| collection | DOAJ |
| description | With ultra-high density and preservation longevity, deoxyribonucleic acid (DNA)-based data storage is becoming an emerging storage technology. Limited by the current biochemical techniques, data might be corrupted during the processes of DNA data storage. A hybrid coding architecture consisting of modified variable-length run-length limited (VL-RLL) codes and optimized protograph low-density parity-check (LDPC) codes is proposed in order to suppress error occurrence and correct asymmetric substitution errors. Based on the analyses of the different asymmetric DNA sequencer channel models, a series of the protograph LDPC codes are optimized using a modified extrinsic information transfer algorithm (EXIT). The simulation results show the better error performance of the proposed protograph LDPC codes over the conventional good codes and the codes used in the existing DNA data storage system. In addition, the theoretical analysis shows that the proposed hybrid coding scheme stores ~1.98 bits per nucleotide (bits/nt) with only 1% gap from the upper boundary (2 bits/nt). |
| first_indexed | 2024-12-16T17:59:53Z |
| format | Article |
| id | doaj.art-e1e7fc8d739847eb8b21742f6aef2ba7 |
| institution | Directory Open Access Journal |
| issn | 2169-3536 |
| language | English |
| last_indexed | 2024-12-16T17:59:53Z |
| publishDate | 2019-01-01 |
| publisher | IEEE |
| record_format | Article |
| series | IEEE Access |
| spelling | doaj.art-e1e7fc8d739847eb8b21742f6aef2ba72022-12-21T22:22:05ZengIEEEIEEE Access2169-35362019-01-017841078412110.1109/ACCESS.2019.29248278746106Optimized Code Design for Constrained DNA Data Storage With Asymmetric ErrorsLi Deng0https://orcid.org/0000-0002-9478-551XYixin Wang1MD. Noor-A-Rahim2Yong Liang Guan3Zhiping Shi4Erry Gunawan5Chueh Loo Poh6National Key Laboratory of Science and Technology on Communications, University of Electronic Science and Technology of China, Chengdu, ChinaSchool of Electrical and Electronic Engineering, Nanyang Technological University, SingaporeSchool of Computer Science and IT, University College Cork, Cork, IrelandSchool of Electrical and Electronic Engineering, Nanyang Technological University, SingaporeNational Key Laboratory of Science and Technology on Communications, University of Electronic Science and Technology of China, Chengdu, ChinaSchool of Electrical and Electronic Engineering, Nanyang Technological University, SingaporeDepartment of Biomedical Engineering, National University of Singapore, SingaporeWith ultra-high density and preservation longevity, deoxyribonucleic acid (DNA)-based data storage is becoming an emerging storage technology. Limited by the current biochemical techniques, data might be corrupted during the processes of DNA data storage. A hybrid coding architecture consisting of modified variable-length run-length limited (VL-RLL) codes and optimized protograph low-density parity-check (LDPC) codes is proposed in order to suppress error occurrence and correct asymmetric substitution errors. Based on the analyses of the different asymmetric DNA sequencer channel models, a series of the protograph LDPC codes are optimized using a modified extrinsic information transfer algorithm (EXIT). The simulation results show the better error performance of the proposed protograph LDPC codes over the conventional good codes and the codes used in the existing DNA data storage system. In addition, the theoretical analysis shows that the proposed hybrid coding scheme stores ~1.98 bits per nucleotide (bits/nt) with only 1% gap from the upper boundary (2 bits/nt).https://ieeexplore.ieee.org/document/8746106/DNA data storageprotograph LDPC codesasymmetric substitutionsconstrained codesDNA sequencing |
| spellingShingle | Li Deng Yixin Wang MD. Noor-A-Rahim Yong Liang Guan Zhiping Shi Erry Gunawan Chueh Loo Poh Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors IEEE Access DNA data storage protograph LDPC codes asymmetric substitutions constrained codes DNA sequencing |
| title | Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors |
| title_full | Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors |
| title_fullStr | Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors |
| title_full_unstemmed | Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors |
| title_short | Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors |
| title_sort | optimized code design for constrained dna data storage with asymmetric errors |
| topic | DNA data storage protograph LDPC codes asymmetric substitutions constrained codes DNA sequencing |
| url | https://ieeexplore.ieee.org/document/8746106/ |
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