Related papers: Clustering-Correcting Codes
This paper introduces a new solution to DNA storage that integrates all three steps of retrieval, namely clustering, reconstruction, and error correction. DNA-correcting codes are presented as a unique solution to the problem of ensuring…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
In this paper, we study error-correcting codes for the storage of data in synthetic deoxyribonucleic acid (DNA). We investigate a storage model where data is represented by an unordered set of $M$ sequences, each of length $L$. Errors…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
Motivated by DNA-based data storage, we investigate a system where digital information is stored in an unordered set of several vectors over a finite alphabet. Each vector begins with a unique index that represents its position in the whole…
In this paper, we study achievable rates of concatenated coding schemes over a deoxyribonucleic acid (DNA) storage channel. Our channel model incorporates the main features of DNA-based data storage. First, information is stored on many,…
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…
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…
To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…
The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
Error-correcting codes over sets, with applications to DNA storage, are studied. The DNA-storage channel receives a set of sequences, and produces a corrupted version of the set, including sequence loss, symbol substitution, symbol…
Motivated by DNA based data storage system, we investigate the errors that occur when synthesizing DNA strands in parallel, where each strand is appended one nucleotide at a time by the machine according to a template supersequence. If…
Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the…
As a medium for cold data storage, DNA stands out as it promises significant gains in storage capacity and lifetime. However, it comes with its own data processing challenges to overcome. Constrained codes over the DNA alphabet…
We consider error-correcting coding for DNA-based storage. We model the DNA storage channel as a multi-draw IDS channel where the input data is chunked into $M$ short DNA strands, which are copied a random number of times, and the channel…
Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and…