Related papers: DNA codes from $(\text{\textbaro}, \mathfrak{d}, \…
Let $\mathbb{Z}_p$ be the ring of integers modulo a prime number $p$ where $p-1$ is a quadratic residue modulo $p$. This paper presents the study of constacyclic codes over chain rings $\mathcal{R}=\frac{\mathbb{Z}_p[u]}{\langle…
We present new constructions of codes for asymmetric channels for both binary and nonbinary alphabets, based on methods of generalized code concatenation. For the binary asymmetric channel, our methods construct nonlinear…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
In this paper, we construct new families of convolutional codes. Such codes are obtained by means of algebraic geometry codes. Additionally, more families of convolutional codes are constructed by means of puncturing, extending, expanding…
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…
In this paper, we study $\mathbb{Z}_{2}\mathbb{Z}_{2}[u]$-$(1+u)$-additive constacyclic code of arbitrary length. Firstly, we study the algebraic structure of this family of codes and a set of generator polynomials for this family as a…
Let $\mathbb{F}_{p^m}$ be a finite field of cardinality $p^m$, where $p$ is a prime, and $k, N$ be any positive integers. We denote $R_k=F_{p^m}[u]/\langle u^k\rangle =F_{p^m}+uF_{p^m}+\ldots+u^{k-1}F_{p^m}$ ($u^k=0$) and…
A method for encoding information in DNA sequences is described. The method is based on the precision-resolution framework, and is aimed to work in conjunction with a recently suggested terminator-free template independent DNA synthesis…
$(1+pw)$-constacyclic codes of arbitrary length over the non-principal ideal ring $\mathbb{Z}_{p^s} +u\mathbb{Z}_{p^s}$ are studied, where $p$ is a prime, $w\in \mathbb{Z}_{p^s}^{\times}$ and $s$ an integer satisfying $s\geq 2$. First, the…
The rings $Z_{4}+\nu Z_{4}$ have been classified into chain rings and non-chain rings on the basis of the values of $\nu^{2} \in Z_{4}+\nu Z_{4}.$ In this paper, the structure of cyclic codes of arbitrary length over the rings $Z_{4}+\nu…
DNA based storage systems received attention by many researchers. This includes archival and re-writable random access DNA based storage systems. In this work, we have developed an efficient technique to encode the data into DNA sequence by…
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…
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…
DNA, with remarkable properties of high density, durability, and replicability, is one of the most appealing storage media. Emerging DNA storage technologies use composite DNA letters, where information is represented by probability…
We propose coding techniques that limit the length of homopolymers runs, ensure the GC-content constraint, and are capable of correcting a single edit error in strands of nucleotides in DNA-based data storage systems. In particular, for…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
In this work, we study a class of skew cyclic codes over the ring $R:=\mathbb{Z}_4+v\mathbb{Z}_4,$ where $v^2=v,$ with an automorphism $\theta$ and a derivation $\Delta_\theta,$ namely codes as modules over a skew polynomial ring…
The purpose of this article is to study constacyclic codes of length $np^s$ over $R^t:=\frac{\mathbb{F}_{p^m}[u]}{\langle u^t \rangle },$ where $t$ is a natural number and $\gcd(n,p)=1$. We give generators of all the ideals of…
In this paper, the investigation on the algebraic structure of the ring $\frac{\mathbb{F}_q[v]}{\langle\,v^q-v\,\rangle}$ and the description of its automorphism group, enable to study the algebraic structure of codes and their dual over…
We consider the problem of assembling a sequence based on a collection of its substrings observed through a noisy channel. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on…