MO4.R6.2

Efficient DNA Synthesis Codes with Error Correction and Runlength Limited Constraint

Tuan Thanh Nguyen, Kui Cai, Singapore University of Technology and Design, Singapore; Schouhamer Immink Kees, Turing Machines Inc, Netherlands

Session:
DNA storage and coding

Track:
17: Information and Coding in Biology

Location:
Sigma/Delta

Presentation Time:
Mon, 8 Jul, 16:45 - 17:05

Session Chair:
Eitan Yaakobi, Technion -- Israel Institute of Technology
Abstract
DNA synthesis remains the most costly part of the DNA data storage. In this work, we consider a popular synthesis method that generates multiple DNA strands in parallel from a fixed supersequence S, one nucleotide at a time. Under this assumption, the synthesis time (or the number of synthesis cycles) is then determined by the length of the common supersequence. In this work, we propose constructions of quaternary codes that simultaneously (i) restrict the maximum synthesis time, (ii) correct a single deletion or insertion error, and (iii) satisfy the runlength limited constraint, a crucial biochemical constraint in a DNA storage channel. For certain parameters, we provide an improved construction of DNA codes with a smaller synthesis time while costing less redundancy as compared to the best-known result in the literature.
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