Construction of Bio-Constrained Code for DNA Data Storage

• Published in: IEEE communications letters Vol. 23; no. 6; pp. 963 - 966
• Main Authors: Wang, Yixin, Noor-A-Rahim, Md, Gunawan, Erry, Guan, Yong Liang, Poh, Chueh Loo
• Format: Journal Article
• Language: English
• Published: New York IEEE 01.06.2019; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: 3G mobile communication; Binary data; Coding; Complexity; Complexity theory; constrained code; Constraints; Data storage; Deoxyribonucleic acid; DNA; DNA data storage; Gene sequencing; long term data storage; Memory; Precoding; run-length limited code; Silicon; Storage systems
• ISSN: 1089-7798; 1558-2558
• DOI: 10.1109/LCOMM.2019.2912572

With extremely high density and durable preservation, DNA data storage has become one of the most cutting-edge techniques for long-term data storage. Similar to traditional storage which impose restrictions on the form of encoded data, data stored in DNA storage systems are also subject to two biochemical constraints, i.e., maximum homopolymer run limit and balanced GC content limit. Previous studies used successive process to satisfy these two constraints. As a result, the process suffers low efficiency and high complexity. In this letter, we propose a novel content-balanced run-length limited code with an efficient code construction method, which generates short DNA sequences that satisfy both constraints at one time. Besides, we develop an encoding method to map binary data into long DNA sequences for DNA data storage, which ensures both local and global stability in terms of satisfying the biochemical constraints. The proposed encoding method has high effective code rate of 1.917 bits per nucleotide and low coding complexity.