Related papers: Coding for Strand Breaks in Composite DNA
In order to provide high data reliability, distributed storage systems disperse data with redundancy to multiple storage nodes. Regenerating codes is a new class of erasure codes to introduce redundancy for the purpose of improving the data…
In database design, Composite Keys are used to uniquely identify records and prevent data duplication. However, they require more memory and storage space than single keys, and can make queries more CPU-intensive. Surrogate Keys are an…
DNA codes have many applications, such as in data storage, DNA computing, etc. Good DNA codes have large sizes and satisfy some certain constraints. In this paper, we present a new construction method for reversible DNA codes. We show that…
Classical erasure codes, e.g. Reed-Solomon codes, have been acknowledged as an efficient alternative to plain replication to reduce the storage overhead in reliable distributed storage systems. Yet, such codes experience high overhead…
In this paper, we investigate the optimum way to allocate redundancy of finite-length nested codes for modern nonvolatile memories suffering from both permanent defects and transient errors (erasures or random errors). A nested coding…
The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS) errors, as well as sequence-level…
We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…
Oxidative DNA single strand breaks arise continuously in cells and defects in their repair have been implicated in neurological disease. While much progress has been made in understanding how chromosomal single strand breaks are repaired…
Reconstruction codes are generalizations of error-correcting codes that can correct errors by a given number of noisy reads. The study of such codes was initiated by Levenshtein in 2001 and developed recently due to applications in modern…
DNA-based data storage has been attracting significant attention due to its extremely high data storage density, low power consumption, and long duration compared to conventional data storage media. Despite the recent advancements in DNA…
The DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For…
As sensing and instrumentation play an increasingly important role in systems controlled over wired and wireless networks, the need to better understand delay-sensitive communication becomes a prime issue. Along these lines, this article…
Channel coding alone is not sufficient to reliably transmit a message of finite length $K$ from a source to one or more destinations as in, e.g., file transfer. To ensure that no data is lost, it must be combined with rateless erasure…
Several types of AL-FEC (Application-Level FEC) codes for the Packet Erasure Channel exist. Random Linear Codes (RLC), where redundancy packets consist of random linear combinations of source packets over a certain finite field, are a…
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 problem of string reconstruction based on its substrings spectrum has received significant attention recently due to its applicability to DNA data storage and sequencing. In contrast to previous works, we consider in this paper a setup…
We present a Compression Tool, "GenBit Compress", for genetic sequences based on our new proposed "GenBit Compress Algorithm". Our Tool achieves the best compression ratios for Entire Genome (DNA sequences) . Significantly better…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…
This paper presents a novel coding scheme for distributed storage systems containing nodes with adversarial errors. The key challenge in such systems is the propagation of erroneous data from a single corrupted node to the rest of the…
The recently proposed compressed backbone theory suggested that the intrinsic curvature in DNA can result from a geometric mismatch between the specific backbone length and optimal base stacking orientations. It predicted that the curvature…