A robust and efficient DNA storage architecture based on modulation encoding and decoding
Open accessAbstract
Thanks to its high density and long durability, synthetic DNA has been widely considered as a promising solution to the data explosion problem. However, due to the large amount of random base insertion-deletion-substitution (IDSs) errors from sequencing, reliable data recovery remains a critical challenge, which hinders its large-scale application. Here, we propose a modulation-based DNA storage architecture. Experiments on simulation and real datasets demonstrate that it has two distinct advantages. First, modulation encoding provides a simple way to ensure the encoded DNA sequences comply with biological sequence constraints (i.e., GC balanced and no homopolymers); Second, modulation decoding is highly efficient and extremely robust for the detection of insertions and deletions, which can correct up to ~40% errors. These two advantages pave the way for future high-throughput and low-cost techniques, and will kickstart the actualization of a viable, large-scale system for DNA data storage.
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In the high error regime, the modulation-based method proposed by our group is perhaps the best solution today, as it could correct up to 40% errors.
“In the high error regime, the modulation-based method proposed by our group is perhaps the best solution today, as it could correct up to 40% errors.”
From Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage (2023) · cites this paper as [19]
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Self-citation
- Authors
- Zan, X., Xie, R., Yao, X., Xu, P., & Liu, W.
- Affiliations
- Guangzhou University (CN)
- Corresponding author
- Xu, Peng
- Liu, Wenbin
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- openRxiv
- Published
- 2022-05-25
- Volume
- 63
- Issue
- 12
- Pages
- 3967-3976
- ISSN
- 1549-9596 (ISSN-L)
- OpenAlex
- W4379769333
- Cited by
- 27
- References
- 33
- Citations by year
- 2026: 7 · 2025: 7 · 2024: 9 · 2023: 3 · 2022: 1
- FWCI
- 2.31
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- Journal of Chemical Information and Modeling (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- Funders
- National Natural Science Foundation of China (62002079, 62072128)
- Natural Science Foundation of Guangdong Province (2023A1515011401)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- DNA data storage, synthetic DNA, error detection, storage density
- MeSH terms
- Computer Simulation, DNA, Information Storage and Retrieval, Sequence Analysis, DNA
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