Optimized code design for constrained DNA data storage with asymmetric errors

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dc.contributor.authorDeng, Li
dc.contributor.authorWang, Yixin
dc.contributor.authorNoor-A-Rahim, Md.
dc.contributor.authorGuan, Yong Liang
dc.contributor.authorShi, Zhiping
dc.contributor.authorGunawan, Erry
dc.contributor.authorPoh, Chueh Loo
dc.contributor.funderNational Natural Science Foundation of Chinaen
dc.contributor.funderNatural Science Foundation of Guangxi Provinceen
dc.contributor.funderEuropean Commissionen
dc.date.accessioned2019-09-16T08:58:28Z
dc.date.available2019-09-16T08:58:28Z
dc.date.issued2019-06-26
dc.description.abstractWith 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).en
dc.description.sponsorshipNatural Science Foundation of China (Grant 61671128); Sichuan Key Research and Development Project (Grant 2019YFG0105); Guangxi Natural Science Foundation (Grant 2018GXNSFAA281161); Guangxi Education Department Youth Science Foundation (Grant 2019KY0796).en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationDeng, L., Wang, Y., Noor-A-Rahim, M., Guan, Y. L., Shi, Z., Gunawan, E. and Poh, C. L. (2019) 'Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors', IEEE Access, 7, pp. 84107-84121. (14pp.) DOI: 10.1109/ACCESS.2019.2924827en
dc.identifier.doi10.1109/ACCESS.2019.2924827en
dc.identifier.eissn2169-3536
dc.identifier.endpage84121en
dc.identifier.journaltitleIEEE Accessen
dc.identifier.startpage84107en
dc.identifier.urihttps://hdl.handle.net/10468/8531
dc.identifier.volume7en
dc.language.isoenen
dc.publisherInstitute of Electrical and Electronics Engineers Inc.en
dc.relation.projectinfo:eu-repo/grantAgreement/EC/H2020::MSCA-COFUND-FP/713567/EU/Cutting Edge Training - Cutting Edge Technology/EDGEen
dc.relation.urihttps://ieeexplore.ieee.org/document/8746106/figures#figures
dc.rights©This work is licensed under a Creative Commons Attribution 3.0 License. For more information, see http://creativecommons.org/licenses/by/3.0/en
dc.rights.urihttps://creativecommons.org/licenses/by/3.0/en
dc.subjectChannel codingen
dc.subjectDNAen
dc.subjectParity check codesen
dc.subjectRunlength codesen
dc.subjectDNA data storage systemen
dc.subjectAsymmetric DNA sequencer channel modelsen
dc.subjectHybrid coding scheme storesen
dc.subjectError performanceen
dc.subjectModified extrinsic information transfer algorithmen
dc.subjectProtograph LDPC codesen
dc.subjectCorrect asymmetric substitution errorsen
dc.subjectError occurrenceen
dc.subjectOptimized protograph low-density parity-check codesen
dc.subjectModified variable-length run-lengthen
dc.subjectHybrid coding architectureen
dc.subjectDeoxyribonucleic acid-based data storageen
dc.subjectAsymmetric errorsen
dc.subjectConstrained DNA data storageen
dc.subjectMemoryen
dc.subjectEncodingen
dc.subjectSequential analysisen
dc.subjectDecodingen
dc.subjectData storage systemsen
dc.subjectDNA data storageen
dc.subjectAsymmetric substitutionsen
dc.subjectConstrained codesen
dc.subjectDNA sequencingen
dc.titleOptimized code design for constrained DNA data storage with asymmetric errorsen
dc.typeArticle (peer-reviewed)en
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