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Title: Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors
Authors: Deng, L.
Wang, Y.
Noor-A-Rahim, M.D.
Guan, Y.L.
Shi, Z.
Gunawan, E.
Poh, C.L. 
Keywords: asymmetric substitutions
constrained codes
DNA data storage
DNA sequencing
protograph LDPC codes
Issue Date: 2019
Publisher: Institute of Electrical and Electronics Engineers Inc.
Citation: Deng, L., Wang, Y., Noor-A-Rahim, M.D., Guan, Y.L., Shi, Z., Gunawan, E., Poh, C.L. (2019). Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors. IEEE Access 7 : 84107-84121. ScholarBank@NUS Repository.
Rights: Attribution-NonCommercial-NoDerivatives 4.0 International
Abstract: 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). © 2013 IEEE.
Source Title: IEEE Access
ISSN: 21693536
DOI: 10.1109/ACCESS.2019.2924827
Rights: Attribution-NonCommercial-NoDerivatives 4.0 International
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