Year: 2024
Type: conference-paper
Abstract: Motivated by DNA based data storage system, we investigate errors that occur when synthesizing DNA strands in parallel, where each strand is appended one nucleotide at a time by the machine according to a template supersequence. If there is a cycle such that the machine fails, then the strands meant to be appended at this cycle will not be appended, and we refer to this as a synthesis defect. In this paper, we present two families of codes correcting these synthesis defects, which are t-known-synthesis-defect correcting codes and t-synthesis-defect correcting codes. For the first one, it is assumed that the defective cycles are known, and each of the codeword is a quaternary sequence. We provide constructions for this family of codes for$t=1,2$, with redundancy log 4 and$2\log n+O(1)$, respectively. For the second one, the codeword is a set of$M$ordered sequences, and we give a construction for$t=1$to show a strategy for constructing this family of codes. Finally, we derive a lower bound on the redundancy for single-known-synthesis-defect correcting codes, which assures that our construction is almost optimal.
Institutions: Shandong University, Nanyang Technological University, ETH Zurich
Language: English
Subfield: Artificial Intelligence
Field: Computer Science
Domain: Physical Sciences
Open Access status: green
Award: G8377584638
OpenAlex ID: W4405908516