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...
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Autor*in:	Li Deng [verfasserIn] Yixin Wang [verfasserIn] MD. Noor-A-Rahim [verfasserIn] Yong Liang Guan [verfasserIn] Zhiping Shi [verfasserIn] Erry Gunawan [verfasserIn] Chueh Loo Poh [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2019

Schlagwörter:	DNA data storage protograph LDPC codes asymmetric substitutions constrained codes DNA sequencing

Übergeordnetes Werk:	In: IEEE Access - IEEE, 2014, 7(2019), Seite 84107-84121
Übergeordnetes Werk:	volume:7 ; year:2019 ; pages:84107-84121

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DOI / URN:	10.1109/ACCESS.2019.2924827

Katalog-ID:	DOAJ056475586

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spelling	10.1109/ACCESS.2019.2924827 doi (DE-627)DOAJ056475586 (DE-599)DOAJe1e7fc8d739847eb8b21742f6aef2ba7 DE-627 ger DE-627 rakwb eng TK1-9971 Li Deng verfasserin aut Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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). DNA data storage protograph LDPC codes asymmetric substitutions constrained codes DNA sequencing Electrical engineering. Electronics. Nuclear engineering Yixin Wang verfasserin aut MD. Noor-A-Rahim verfasserin aut Yong Liang Guan verfasserin aut Zhiping Shi verfasserin aut Erry Gunawan verfasserin aut Chueh Loo Poh verfasserin aut In IEEE Access IEEE, 2014 7(2019), Seite 84107-84121 (DE-627)728440385 (DE-600)2687964-5 21693536 nnns volume:7 year:2019 pages:84107-84121 https://doi.org/10.1109/ACCESS.2019.2924827 kostenfrei https://doaj.org/article/e1e7fc8d739847eb8b21742f6aef2ba7 kostenfrei https://ieeexplore.ieee.org/document/8746106/ kostenfrei https://doaj.org/toc/2169-3536 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2019 84107-84121
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allfieldsSound	10.1109/ACCESS.2019.2924827 doi (DE-627)DOAJ056475586 (DE-599)DOAJe1e7fc8d739847eb8b21742f6aef2ba7 DE-627 ger DE-627 rakwb eng TK1-9971 Li Deng verfasserin aut Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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). DNA data storage protograph LDPC codes asymmetric substitutions constrained codes DNA sequencing Electrical engineering. Electronics. Nuclear engineering Yixin Wang verfasserin aut MD. Noor-A-Rahim verfasserin aut Yong Liang Guan verfasserin aut Zhiping Shi verfasserin aut Erry Gunawan verfasserin aut Chueh Loo Poh verfasserin aut In IEEE Access IEEE, 2014 7(2019), Seite 84107-84121 (DE-627)728440385 (DE-600)2687964-5 21693536 nnns volume:7 year:2019 pages:84107-84121 https://doi.org/10.1109/ACCESS.2019.2924827 kostenfrei https://doaj.org/article/e1e7fc8d739847eb8b21742f6aef2ba7 kostenfrei https://ieeexplore.ieee.org/document/8746106/ kostenfrei https://doaj.org/toc/2169-3536 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2019 84107-84121
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source	In IEEE Access 7(2019), Seite 84107-84121 volume:7 year:2019 pages:84107-84121
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topic_facet	DNA data storage protograph LDPC codes asymmetric substitutions constrained codes DNA sequencing Electrical engineering. Electronics. Nuclear engineering
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authorswithroles_txt_mv	Li Deng @@aut@@ Yixin Wang @@aut@@ MD. Noor-A-Rahim @@aut@@ Yong Liang Guan @@aut@@ Zhiping Shi @@aut@@ Erry Gunawan @@aut@@ Chueh Loo Poh @@aut@@
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callnumber-first	T - Technology
author	Li Deng
spellingShingle	Li Deng misc TK1-9971 misc DNA data storage misc protograph LDPC codes misc asymmetric substitutions misc constrained codes misc DNA sequencing misc Electrical engineering. Electronics. Nuclear engineering Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors
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topic_title	TK1-9971 Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors DNA data storage protograph LDPC codes asymmetric substitutions constrained codes DNA sequencing
topic	misc TK1-9971 misc DNA data storage misc protograph LDPC codes misc asymmetric substitutions misc constrained codes misc DNA sequencing misc Electrical engineering. Electronics. Nuclear engineering
topic_unstemmed	misc TK1-9971 misc DNA data storage misc protograph LDPC codes misc asymmetric substitutions misc constrained codes misc DNA sequencing misc Electrical engineering. Electronics. Nuclear engineering
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title	Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors
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title_sort	optimized code design for constrained dna data storage with asymmetric errors
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title_auth	Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors
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).
abstractGer	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).
abstract_unstemmed	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).
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title_short	Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors
url	https://doi.org/10.1109/ACCESS.2019.2924827 https://doaj.org/article/e1e7fc8d739847eb8b21742f6aef2ba7 https://ieeexplore.ieee.org/document/8746106/ https://doaj.org/toc/2169-3536
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