A Hierarchical Error Correction Strategy for Text DNA Storage

Zan, Xiangzhen; Yao, Xiangyu; Xu, Peng; Chen, Zhihua; Xie, Lei; Li, Shudong; Liu, Wenbin

doi:10.1007/s12539-021-00476-x

Cited by 17 publications

(14 citation statements)

References 39 publications

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“…Errors such as substitution, insertion, and deletion of bases are prone to occur during the synthesis of DNA sequences during DNA storage and DNA sequencing ( Wang et al, 2019 ). The error rate of each base in the DNA sequencing process is about 1% ( Press et al, 2020 ; Zan et al, 2021 ). When there are some special sequences in the DNA sequence (GC content is high in the entire DNA sequence and existence of homopolymers of certain bases), this will easily lead to nonspecific hybridization of DNA during storage ( Wang et al, 2019 ).…”

Section: Encoding Of Hidden Addressingmentioning

confidence: 99%

“…When there are some special sequences in the DNA sequence (GC content is high in the entire DNA sequence and existence of homopolymers of certain bases), this will easily lead to nonspecific hybridization of DNA during storage ( Wang et al, 2019 ). Once the abovementioned hybridization reaction occurs in DNA, it will directly affect the normal progress of the DNA sequencing process, resulting in data read errors and read failures due to sequencing deviations ( Chen Y. J et al, 2020 ; Zan et al, 2021 ). As this situation may easily cause instability of the DNA sequence, the sequence is generally required to comply with the constraints to reduce the incidence of nonspecific hybridization and reduce the error rate in the process of sequence reading and writing.…”

Section: Encoding Of Hidden Addressingmentioning

confidence: 99%

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Hidden Addressing Encoding for DNA Storage

Wang

Sun

et al. 2022

Front. Bioeng. Biotechnol.

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DNA is a natural storage medium with the advantages of high storage density and long service life compared with traditional media. DNA storage can meet the current storage requirements for massive data. Owing to the limitations of the DNA storage technology, the data need to be converted into short DNA sequences for storage. However, in the process, a large amount of physical redundancy will be generated to index short DNA sequences. To reduce redundancy, this study proposes a DNA storage encoding scheme with hidden addressing. Using the improved fountain encoding scheme, the index replaces part of the data to realize hidden addresses, and then, a 10.1 MB file is encoded with the hidden addressing. First, the Dottup dot plot generator and the Jaccard similarity coefficient analyze the overall self-similarity of the encoding sequence index, and then the sequence fragments of GC content are used to verify the performance of this scheme. The final results show that the encoding scheme indexes with overall lower self-similarity, and the local thermodynamic properties of the sequence are better. The hidden addressing encoding scheme proposed can not only improve the utilization of bases but also ensure the correct rate of DNA storage during the sequencing and decoding processes.

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Section: Encoding Of Hidden Addressingmentioning

confidence: 99%

Section: Encoding Of Hidden Addressingmentioning

confidence: 99%

Hidden Addressing Encoding for DNA Storage

Wang

Sun

et al. 2022

Front. Bioeng. Biotechnol.

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“…As the amount of available data grows exponentially, recent developments in synthesis and sequencing technology are making synthetic DNA more attractive as a new data storage medium 1, 2, 3 . Compared with traditional electric/optical/magnetic storage media, DNA synthesis and sequencing are highly error prone processes characterized by aggregated insertions, deletions and substitutions (IDSs) 4 .…”

Section: Introductionmentioning

confidence: 99%

“…Song et al 16 constructed a de Bruijn graph (DBG) using multiple sequences and infer the correct sequence by a graph searching algorithm. For English text storage, our group constructed a 6-base code table for characters and the IDSs were corrected by distance-based code correction, multiple sequence voting, and spelling check 17, 18 . Additionally, Xue et al 19 proposed a special Levenshtein code 20 capable of correcting a single synchronization or substitution error in a code word.…”

Section: Introductionmentioning

confidence: 99%

A robust and efficient DNA storage architecture based on modulation encoding and decoding

Zan

Xie

Yao

et al. 2022

Preprint

Self Cite

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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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“…With the rapid development in storage technology, scientists have proved that Deoxyribonucleic Acid (DNA) is a potential storage medium 21,22,23 . Moreover, due to its high parallelism and enormous information density, DNA-based encryption scheme is considered to be a potential alternative to traditional encryption scheme.…”

Section: Introductionmentioning

confidence: 99%

A novel image encryption scheme for DNA storage systems based on gene hybridization and gene mutation

Yao

Xie

Zan

et al. 2022

Preprint

Self Cite

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With the rapid development of DNA (Deoxyribonucleic Acid) storage technologies, storing digital images in DNA is feasible. Meanwhile, the information security in DNA storage system is still a problem to solve. Therefore, in this paper, we propose a DNA storage-oriented image encryption algorithm utilizing the information processing mechanisms in molecule biology. The basic idea is to perform pixel replacement by gene hybridization, and implement dual diffusion by pixel diffusion and gene mutation. The ciphertext DNA image can be synthesized and stored in DNA storage system after encryption. Experimental results demonstrate it can resist common attacks, and shows a strong robustness in against sequence loss and base substitution errors in the DNA storage channel.

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A Hierarchical Error Correction Strategy for Text DNA Storage

Cited by 17 publications

References 39 publications

Hidden Addressing Encoding for DNA Storage

Hidden Addressing Encoding for DNA Storage

A robust and efficient DNA storage architecture based on modulation encoding and decoding

A novel image encryption scheme for DNA storage systems based on gene hybridization and gene mutation

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