A Segmented-Edit Error-Correcting Code With Re-Synchronization Function for DNA-Based Storage Systems

Yan, Zihui; Liang, Cong; Wu, Huaming

doi:10.1109/tetc.2022.3225570

Cited by 9 publications

(3 citation statements)

References 33 publications

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“…In fountain code, if the error is not corrected or identified, the file cannot be recovered ( Zhang et al, 2021 ). Zihui Yan et al ( Yan et al, 2022a ) . ( Yan et al, 2022b ) proposed a DNA error correction method called DNA segment Levenshtein-Marker (DNA-LM).…”

Section: Resultsmentioning

confidence: 99%

Towards long double-stranded chains and robust DNA-based data storage using the random code system

Shi

Lai

et al. 2023

Front. Genet.

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DNA has become a popular choice for next-generation storage media due to its high storage density and stability. As the storage medium of life’s information, DNA has significant storage capacity and low-cost, low-power replication and transcription capabilities. However, utilizing long double-stranded DNA for storage can introduce unstable factors that make it difficult to meet the constraints of biological systems. To address this challenge, we have designed a highly robust coding scheme called the “random code system,” inspired by the idea of fountain codes. The random code system includes the establishment of a random matrix, Gaussian preprocessing, and random equilibrium. Compared to Luby transform codes (LT codes), random code (RC) has better robustness and recovery ability of lost information. In biological experiments, we successfully stored 29,390 bits of data in 25,700 bp chains, achieving a storage density of 1.78 bits per nucleotide. These results demonstrate the potential for using long double-stranded DNA and the random code system for robust DNA-based data storage.

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Section: Resultsmentioning

confidence: 99%

Towards long double-stranded chains and robust DNA-based data storage using the random code system

Shi

Lai

et al. 2023

Front. Genet.

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“…Currently, to address sequence loss issues, the primary approach involves adding redundant sequences [ 5 , 15 ]. In the early stage, error correction codes were mainly used to correct base errors in sequences, such as RS (Reed-Solomon) codes [ 3 , 16 – 18 ], BCH (Bose-Chaudhuri-Hocquenghem) codes [ 19 ], LDPC (low-density parity-check) codes [ 20 , 21 ], HEDGES (Hash Encoded, Decoded by Greedy Exhaustive Search) error-correcting code [ 22 ], and DNA-Aeon [ 23 ]. Besides, there are also methods available that achieve error correction based on specific constraints [ 24 ] and particular rules [ 25 ].…”

Section: Introductionmentioning

confidence: 99%

DNA-QLC: an efficient and reliable image encoding scheme for DNA storage

Zheng,

Cao,

Zhang

et al. 2024

BMC Genomics

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Background DNA storage has the advantages of large capacity, long-term stability, and low power consumption relative to other storage mediums, making it a promising new storage medium for multimedia information such as images. However, DNA storage has a low coding density and weak error correction ability. Results To achieve more efficient DNA storage image reconstruction, we propose DNA-QLC (QRes-VAE and Levenshtein code (LC)), which uses the quantized ResNet VAE (QRes-VAE) model and LC for image compression and DNA sequence error correction, thus improving both the coding density and error correction ability. Experimental results show that the DNA-QLC encoding method can not only obtain DNA sequences that meet the combinatorial constraints, but also have a net information density that is 2.4 times higher than DNA Fountain. Furthermore, at a higher error rate (2%), DNA-QLC achieved image reconstruction with an SSIM value of 0.917. Conclusions The results indicate that the DNA-QLC encoding scheme guarantees the efficiency and reliability of the DNA storage system and improves the application potential of DNA storage for multimedia information such as images.

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“…If the codewords are not chosen appropriately, unintended (non-selective) hybridization or errors may occur during the process. To address these potential issues and ensure the reliability of DNA storage, numerous exceptional error correction methods [3] , [4] , [5] and DNA clustering methods [6] , [7] have been proposed, which play a crucial role in enhancing the accuracy and efficiency of DNA storage systems, mitigating errors, and ensuring the integrity of the stored digital information.…”

Section: Introductionmentioning

confidence: 99%

On secondary structure avoidance of codes for DNA storage

Zhang,

2024

Computational and Structural Biotechnology Journal

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A Segmented-Edit Error-Correcting Code With Re-Synchronization Function for DNA-Based Storage Systems

Cited by 9 publications

References 33 publications

Towards long double-stranded chains and robust DNA-based data storage using the random code system

Towards long double-stranded chains and robust DNA-based data storage using the random code system

DNA-QLC: an efficient and reliable image encoding scheme for DNA storage

On secondary structure avoidance of codes for DNA storage

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