Half-Marker Codes for Deletion Channels with Applications in DNA Storage

TL;DR

This paper introduces half-marker codes, a new class of synchronization codes for DNA storage systems, which improve error correction and increase mutual information in channels with insertion, deletion, and substitution errors.

Contribution

The paper proposes half-marker codes that reserve one bit for synchronization within each DNA base, enhancing error correction capabilities over standard marker codes.

Findings

Half-marker codes outperform standard marker codes when concatenated with outer error-correcting codes.

They significantly reduce the end-to-end bit error rate in DNA storage channels.

The approach increases mutual information between input symbols and channel outputs.

Abstract

DNA storage systems face significant challenges, including insertion, deletion, and substitution (IDS) errors. Therefore, designing effective synchronization codes, i.e., codes capable of correcting IDS errors, is essential for DNA storage systems. Marker codes are a favorable choice for this purpose. In this paper, we extend the notion of marker codes by making the following key observation. Since each DNA base is equivalent to a 2-bit storage unit, one bit can be reserved for synchronization, while the other is dedicated to data transmission. Using this observation, we propose a new class of marker codes, which we refer to as half-marker codes. We demonstrate that this extension has the potential to significantly increase the mutual information between the input symbols and the soft outputs of an IDS channel modeling a DNA storage system. Specifically, through examples, we show that when concatenated with an outer error-correcting code, half-marker codes outperform standard marker codes and significantly reduce the end-to-end bit error rate of the system.