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

• Published in: BMC genomics Vol. 25; no. 1; pp. 266 - 10
• Main Authors: Zheng, Yanfen, Cao, Ben, Zhang, Xiaokang, Cui, Shuang, Wang, Bin, Zhang, Qiang
• Format: Journal Article
• Language: English
• Published: London BioMed Central 09.03.2024; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Algorithms; Analysis; Animal Genetics and Genomics; Biomedical and Life Sciences; Codes; Combinatorial analysis; Combinatorial constraint; Density; Deoxyribonucleic acid; DNA; DNA sequencing; Energy consumption; Error correction; Error correction & detection; Gene sequencing; Genetic research; Image coding; Image compression; Image processing; Image reconstruction; Information storage and retrieval; Levenshtein code; Life Sciences; Medical imaging equipment; Methods; Microarrays; Microbial Genetics and Genomics; Multimedia; Net information density; Nucleotide sequence; Nucleotide sequencing; Plant Genetics and Genomics; Power consumption; Proteomics; Reading; China; Net information density; Combinatorial constraint; Levenshtein code; Image reconstruction
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-10178-5

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.