Notice of Violation of IEEE Publication Principles: Construction of GC-Balanced DNA With Deletion/Insertion/Mutation Error Correction for DNA Storage System

Abstract

Synthetic deoxyribonucleic acid (DNA) is a good medium for storing digital data for a long period due to its achievable high data storage density and outstanding longevity. However, synthesizing and sequencing DNA sequences in a DNA storage system are prone to a wide variety of errors, including insertion, deletion and mutation errors a. At the same time, it is known that DNA sequences with 50% GC content are less susceptible to errors. This paper presents the construction of a GC-balanced DNA sequence with error correction capability. A systematic single insertion/deletion/substitution error correction code is first proposed and then used to design a GC-balanced scheme for synthesizing DNA sequences. With the proposed method, DNA sequences with exactly 50% GC content are constructed. Such DNA sequences not only have the maximum endurance to errors, but are able to correct both insertion/deletion and mutation of the nucleotide bases. The decoding procedures for the sequences are described and can readily be used in practice. Simulation results show that the proposed GC-balanced DNA sequences can correct base errors adequately. a Mutation errors occurring in DNA data storage systems are equivalent to substitution errors in conventional data storage and digital communication systems. In this paper, mutation errors and substitution errors may be used interchangeably.

Towards Practical and Robust DNA-Based Data Archiving Using ‘Yin-Yang Codec’ System

“…3D). Although researchers have been aware of this issue and have developed a few specific errorcorrection codes, these strategies need more experimental verification (45)(46)(47). Currently, sequences with insertions or deletions will be treated as lost sequences.…”

Design of Nonbinary Error Correction Codes With a Maximum Run-Length Constraint to Correct a Single Insertion or Deletion Error for DNA Storage

“…Since a DNA strand is subject to two constraints, i.e., balanced GC-content (45%-55%) and short homopolymer length (≤3), which enable low error rates during DNA synthesis and sequencing processes [5], the constrained codes [4], [11] without the capability of error correction have been considered to reduce the occurrence of insertion, deletion, and substitution errors in DNA storage. Furthermore, the constrained code combined with the error correction code has been considered for DNA storage [12].…”

“…The authors of [16] proposed an efficient systematic encoding algorithm for nonbinary SIDEC codes whose codewords consist of parity symbols and message symbols. A binary EVT code combined with a GC-balanced constrained code [12] and a binary VT code combined with a GC-balanced and r run-length limited constrained code [17] were applied for DNA storage systems. Additionally, a new binary SIDEC code combined with the maximum runlength r constrained code and efficient systematic encoding algorithm was proposed in [18].…”

“…All of these studies [8], [9], [11], [12], [17] focused on binary coding schemes for DNA storage systems. So far, there have been few studies focusing on q-ary coding schemes [19] for DNA storage systems.…”

Channel Model with Memory for DNA Data Storage with Nanopore Sequencing

“…The paper also addresses the design of efficient errorcorrection solutions for DNA storage. Apart from substitutions, most existing practical error-correction codes can correct only insertions [8], or only deletions [8], [9]. Existing solutions [10] which can efficiently correct the three types of errors have a very high complexity, except for the i.i.d.…”