Protecting the Future of Information: LOCO Coding With Error Detection for DNA Data Storage

TL;DR

This paper introduces D-LOCO codes, a novel constrained coding scheme for DNA data storage that enhances error detection, balancing, and efficiency, addressing key challenges in DNA-based information preservation.

Contribution

The paper presents D-LOCO codes with an efficient encoding-decoding rule, balancing capabilities, and error detection schemes, advancing DNA data storage reliability and performance.

Findings

D-LOCO codes achieve capacity and high rates at moderate lengths.

Encoding-decoding algorithms outperform existing methods in storage overhead.

Proposed schemes enable single substitution error detection per codeword.

Abstract

DNA strands serve as a storage medium for $4$-ary data over the alphabet $\{A,T,G,C\}$. DNA data storage promises formidable information density, long-term durability, and ease of replicability. However, information in this intriguing storage technology might be corrupted. Experiments have revealed that DNA sequences with long homopolymers and/or with low $GC$-content are notably more subject to errors upon storage. This paper investigates the utilization of the recently-introduced method for designing lexicographically-ordered constrained (LOCO) codes in DNA data storage. This paper introduces DNA LOCO (D-LOCO) codes, over the alphabet $\{A,T,G,C\}$ with limited runs of identical symbols. These codes come with an encoding-decoding rule we derive, which provides affordable encoding-decoding algorithms. In terms of storage overhead, the proposed encoding-decoding algorithms outperform those in the existing literature. Our algorithms are readily reconfigurable. D-LOCO codes are intrinsically balanced, which allows us to achieve balancing over the entire DNA strand with minimal rate penalty. Moreover, we propose four schemes to bridge consecutive codewords, three of which guarantee single substitution error detection per codeword. We examine the probability of undetecting errors. We also show that D-LOCO codes are capacity-achieving and that they offer remarkably high rates at moderate lengths.