Related papers: Error Correction for DNA Storage
Distributed storage systems and associated storage codes can efficiently store a large amount of data while ensuring that data is retrievable in case of node failure. The study of such systems, particularly the design of storage codes over…
DNA is a promising medium for digital information storage for its exceptional density and durability. While prior studies advanced coding theory, workflow design, and simulation tools, challenges such as synthesis costs, sequencing errors,…
Deoxyribonucleic acid (DNA) has shown great promise in enabling computational applications, most notably in the fields of DNA digital data storage and DNA computing. Information is encoded as DNA strands, which will naturally bind in…
In this paper, we study the Random Access Problem in DNA storage, which addresses the challenge of retrieving a specific information strand from a DNA-based storage system. In this framework, the data is represented by $k$ information…
Secure storage of noisy data for authentication purposes usually involves the use of error correcting codes. We propose a new model scenario involving burst errors and present for that several constructions.
We study the combination of two recent coding approaches, in the context of DNA based data storage. Composite DNA alphabets leverage properties of the DNA synthesis and sequencing process. A composite symbol does not represent a single…
This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…
In recent years, the emergence of DNA storage systems has led to a widespread focus on the research of codes correcting insertions, deletions, and classic substitutions. During the initial investigation, Levenshtein discovered the VT codes…
Encoding information in combinations of pre-synthesised deoxyribonucleic acid (DNA) strands (referred to as motifs) is an interesting approach to DNA storage that could potentially circumvent the prohibitive costs of…
Correcting insertions/deletions as well as substitution errors simultaneously plays an important role in DNA-based storage systems as well as in classical communications. This paper deals with the fundamental task of constructing codes that…
DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have…
Distributed storage systems support failures of individual devices by the use of replication or erasure correcting codes. While erasure correcting codes offer a better storage efficiency than replication for similar fault tolerance, they…
Erasure coding techniques are used to increase the reliability of distributed storage systems while minimizing storage overhead. Also of interest is minimization of the bandwidth required to repair the system following a node failure. In a…
Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (~50,000 bases) in contrast to most current short-read sequencing technologies which can only read hundreds of bases. While nanopore…
The continuously increasing amount of digital data generated by today's society asks for better storage solutions. This survey looks at a new generation of coding techniques designed specifically for the needs of distributed networked…
Deoxyribonucleic acid (DNA) has emerged as a promising building block for next-generation ultra-high density storage devices. Although DNA has high durability and extremely high density in nature, its potential as the basis of storage…
As consumers are increasingly engaged in social networking and E-commerce activities, businesses grow to rely on Big Data analytics for intelligence, and traditional IT infrastructures continue to migrate to the cloud and edge, these trends…
In a distributed storage system, code symbols are dispersed across space in nodes or storage units as opposed to time. In settings such as that of a large data center, an important consideration is the efficient repair of a failed node.…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
The interest in channel models in which the data is sent as an unordered set of binary strings has increased lately, due to emerging applications in DNA storage, among others. In this paper we analyze the minimal redundancy of binary codes…