Efficient and low-complexity variable-to-variable length coding for DNA storage

• Published in: BMC bioinformatics Vol. 25; no. 1; pp. 320 - 14
• Main Authors: Gao, Yunfei, No, Albert
• Format: Journal Article
• Language: English
• Published: London BioMed Central 01.10.2024; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Algorithms; Analysis; Base Composition; Bioinformatics; Biomedical and Life Sciences; Codes; Complexity; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Constraints; Data compression; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA biosynthesis; DNA sequencing; DNA storage; GC content constraint; Gene sequencing; Genetic research; Homopolymer constraint; Information Storage and Retrieval - methods; Life Sciences; Methods; Microarrays; Nucleotide sequence; Nucleotide sequencing; Polymers; Random variables; Sequence Analysis, DNA - methods; Storage systems; Variable-to-variable length code; China; GC content constraint; Homopolymer constraint; DNA storage; Variable-to-variable length code
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-024-05943-y

Background Efficient DNA-based storage systems offer substantial capacity and longevity at reduced costs, addressing anticipated data growth. However, encoding data into DNA sequences is limited by two key constraints: 1) a maximum of h consecutive identical bases (homopolymer constraint h ), and 2) a GC ratio between [ 0.5 - c GC , 0.5 + c GC ] (GC content constraint c GC ). Sequencing or synthesis errors tend to increase when these constraints are violated. Results In this research, we address a pure source coding problem in the context of DNA storage, considering both homopolymer and GC content constraints. We introduce a novel coding technique that adheres to these constraints while maintaining linear complexity for increased block lengths and achieving near-optimal rates. We demonstrate the effectiveness of the proposed method through experiments on both randomly generated data and existing files. For example, when h = 4 and c GC = 0.05 , the rate reached 1.988, close to the theoretical limit of 1.990. The associated code can be accessed at GitHub. Conclusion We propose a variable-to-variable-length encoding method that does not rely on concatenating short predefined sequences, which achieves near-optimal rates.