Related papers: New Constructions of Reversible DNA Codes
Maximum-distance-separable (MDS) codes are a class of erasure codes that are widely adopted to enhance the reliability of distributed storage systems (DSS). In (n, k) MDS coded DSS, the original data are stored into n distributed nodes in…
A simple DNA-based data storage scheme is demonstrated in which information is written using "addressing" oligonucleotides. In contrast to other methods that allow arbitrary code to be stored, the resulting DNA is suitable for downstream…
The explosion in the volumes of data being stored online has resulted in distributed storage systems transitioning to erasure coding based schemes. Local Reconstruction Codes (LRCs) have emerged as the codes of choice for these…
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…
In this short note we give a new upper bound for the size of a set family with a single Hamming distance. Our proof is an application of the linear algebra bound method.
The structures of cyclic DNA codes of odd length over the finite rings R=Z_{4}+wZ_{4}, w^{2}=2 and S=Z_{4}+wZ_{4}+vZ_{4}+wvZ_{4},w^{2}=2,v^{2}=v,wv=vw are studied. The links between the elements of the rings R, S and 16 and 256 codons are…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
Using basic properties of p-adic numbers, we consider a simple new approach to describe main aspects of DNA sequence and genetic code. Central role in our investigation plays an ultrametric p-adic information space which basic elements are…
We show an interesting PBD-closure result for the set of lengths of constant-composition codes whose distance and size meet certain conditions. A consequence of this PBD-closure result is that the size of optimal constant-composition codes…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
In the near future, all the human genes will be identified. But understanding the functions coded in the genes is a much harder problem. For example, by using block entropy, one has that the DNA code is closer to a random code then written…
We present new upper bounds on the parameters of batch codes with restricted query size. These bounds are an improvement on the Singleton bound. The techniques for derivations of these bounds are based on the ideas in the literature for…
The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…
A covering code is a set of codewords with the property that the union of balls, suitably defined, around these codewords covers an entire space. Generally, the goal is to find the covering code with the minimum size codebook. While most…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
A basic problem in constant dimension subspace coding is to determine the maximal possible size ${\bf A}_q(n,d,k)$ of a set of $k$-dimensional subspaces in ${\bf F}_q^n$ such that the subspace distance satisfies…
The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…
In this paper we construct new optimal hierarchical locally recoverable codes. Our construction is based on a combination of the ideas of \cite{ballentine2019codes,sasidharan2015codes} with an algebraic number theoretical approach that…
In this paper, a genetic algorithm, one of the evolutionary algorithms optimization methods, is used for the first time for the problem of finding extremal binary self-dual codes. We present a comparison of the computational times between a…