Mutually Uncorrelated Primers for DNA-Based Data Storage

• Published in: IEEE transactions on information theory Vol. 64; no. 9; pp. 6283 - 6296
• Main Authors: Tabatabaei Yazdi, S. M. H., Kiah, Han Mao, Gabrys, Ryan, Milenkovic, Olgica
• Format: Journal Article
• Language: English
• Published: New York IEEE 01.09.2018; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: bioinformatics; Biological information theory; Block codes; channel coding; constrained coding; Data storage; Data storage systems; Deoxyribonucleic acid; Dimers; DNA; DNA-based data storage systems; Electronic devices; Error correction; Gene sequencing; Hamming distance; Memory; Storage systems; Synchronism; Synchronization
• ISSN: 0018-9448; 1557-9654
• DOI: 10.1109/TIT.2018.2792488

We introduce the notion of weakly mutually uncorrelated (WMU) sequences, motivated by applications in DNA-based data storage systems and synchronization between communication devices. WMU sequences are characterized by the property that no sufficiently long suffix of one sequence is the prefix of the same or another sequence. WMU sequences used for primer design in DNA-based data storage systems are also required to be at large mutual Hamming distance from each other, have balanced compositions of symbols, and avoid primer-dimer byproducts. We derive bounds on the size of WMU and various constrained WMU codes and present a number of constructions for balanced, error-correcting, primer-dimer free WMU codes using Dyck paths, prefix-synchronized, and cyclic codes.