Constrained Error-Correcting Codes for Efficient DNA Synthesis
Information Theory
2025-05-13 v3 math.IT
Abstract
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we propose constrained codes with polynomial-time encoding and decoding algorithms. Compared to the existing works, our codes simultaneously satisfy both l-runlength limited and {\epsilon}-balanced constraints. By enumerating all valid sequences, our codes achieve the maximum rate, matching the capacity. Additionally, we design constrained error-correcting codes capable of correcting one insertion or deletion in the obtained DNA sequence while still adhering to the constraints.
Cite
@article{arxiv.2504.09950,
title = {Constrained Error-Correcting Codes for Efficient DNA Synthesis},
author = {Yajuan Liu and Tolga M. Duman},
journal= {arXiv preprint arXiv:2504.09950},
year = {2025}
}