Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/142420
Title: High capacity DNA data storage with variable-length Oligonucleotides using repeat accumulate code and hybrid mapping
Authors: Wang, Yixin
Md. Noor-A-Rahim
Zhang, Jingyun
Gunawan, Erry
Guan, Yong Liang
Poh, Chueh Loo
Keywords: Engineering::Electrical and electronic engineering
Issue Date: 2019
Source: Wang, Y., Md. Noor-A-Rahim., Zhang, J., Gunawan, E., Guan, Y. L., & Poh, C. L. (2019). High capacity DNA data storage with variable-length Oligonucleotides using repeat accumulate code and hybrid mapping. Journal of Biological Engineering, 13(1), 89-. doi:10.1186/s13036-019-0211-2
Journal: Journal of Biological Engineering
Abstract: Background: With the inherent high density and durable preservation, DNA has been recently recognized as a distinguished medium to store enormous data over millennia. To overcome the limitations existing in a recently reported high-capacity DNA data storage while achieving a competitive information capacity, we are inspired to explore a new coding system that facilitates the practical implementation of DNA data storage with high capacity. Result: In this work, we devised and implemented a DNA data storage scheme with variable-length oligonucleotides (oligos), where a hybrid DNA mapping scheme that converts digital data to DNA records is introduced. The encoded DNA oligos stores 1.98 bits per nucleotide (bits/nt) on average (approaching the upper bound of 2 bits/nt), while conforming to the biochemical constraints. Beyond that, an oligo-level repeat-accumulate coding scheme is employed for addressing data loss and corruption in the biochemical processes. With a wet-lab experiment, an error-free retrieval of 379.1 KB data with a minimum coverage of 10x is achieved, validating the error resilience of the proposed coding scheme. Along with that, the theoretical analysis shows that the proposed scheme exhibits a net information density (user bits per nucleotide) of 1.67 bits/nt while achieving 91% of the information capacity. Conclusion: To advance towards practical implementations of DNA storage, we proposed and tested a DNA data storage system enabling high potential mapping (bits to nucleotide conversion) scheme and low redundancy but highly efficient error correction code design. The advancement reported would move us closer to achieving a practical high-capacity DNA data storage system.
URI: https://hdl.handle.net/10356/142420
ISSN: 1754-1611
DOI: 10.1186/s13036-019-0211-2
Rights: © 2019 The Author(s). This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Fulltext Permission: open
Fulltext Availability: With Fulltext
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