Related papers: On DNA Codes using the Ring Z4 + wZ4

We study quadratic forms over totally real number fields by using an associated ring of quaternions. We examine some properties of residue class rings of these quaternions and use geometry of numbers to prove that certain ideals of the ring…

Binary optimal codes often contain optimal or near-optimal subcodes. In this paper we show that this is true for the family of self-dual codes. One approach is to compute the optimum distance profiles (ODPs) of linear codes, which was…

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…

In this paper, we consider the problem of designing DNA sequences (codewords) for DNA storage systems and DNA computing that are unlikely to fold back onto themselves to form undesirable secondary structures. The paper addresses both the…

Many generator matrices for constructing extremal binary self-dual codes of different lengths have the form G=(I|A), where I is the n by n identity matrix and A is the n by n matrix fully determined by the first row. In this work, we define…

This paper presents a novel method to segment/decode DNA sequences based on n-grams statistical language model. Firstly, we find the length of most DNA 'words' is 12 to 15 bps by analyzing the genomes of 12 model species. Then we design an…

Let k be an arbitrary element of a finite commutative chain ring R and u be a unit in R. In this work, we present necessary conditions which are sufficient as well for a cyclic code to be a (u,k) reversible complement code over R. Using…

We show that our recently published Arithmetic Model of the genetic code based on Godel Encoding is robust against symmetry transformations, specially Rumer s one U > G, A > C, and constitutes a link between the degeneracy structure and the…

Let $R$ be a finite commutative chain ring, $D_{2n}$ be the dihedral group of size $2n$ and $R[D_{2n}]$ be the dihedral group ring. In this paper, we completely characterize left ideals of $R[D_{2n}]$ (called left $D_{2n}$-codes) when ${\rm…

Let $\mathbb{F}_{q}$ be a finite field of cardinality $q$, $R=\mathbb{F}_{q}[u]/\langle u^4\rangle=\mathbb{F}_{q}+u\mathbb{F}_{q}+u^2\mathbb{F}_{q}+u^3\mathbb{F}_{q}$ $(u^4=0)$ which is a finite chain ring, and $n$ be a positive integer…

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…

Inspired by the Z2Z4-additive codes, linear codes over Z2^r x(Z2+uZ2)^s have been introduced by Aydogdu et al. more recently. Although these family of codes are similar to each other, linear codes over Z2^r x(Z2+uZ2)^s have some advantages…

We construct a family of (n,k) convolutional codes with degree \delta in {k,n-k} that have a maximum distance profile. The field size required for our construction is of the order n^{2\delta}, which improves upon the known constructions of…

Linear codes are considered over the ring Z_4+uZ_4, a non-chain extension of Z_4. Lee weights, Gray maps for these codes are defined and MacWilliams identities for the complete, symmetrized and Lee weight enumerators are proved. Two…

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…

This is a review of a set of recent papers with some new data added. After a brief biological introduction a visualization scheme of the string composition of long DNA sequences, in particular, of bacterial complete genomes, will be…

Let $R=\mathbb{Z}_4$ be the integer ring mod $4$. A double cyclic code of length $(r,s)$ over $R$ is a set that can be partitioned into two parts that any cyclic shift of the coordinates of both parts leaves invariant the code. These codes…

For each r, 0 <= r <= m, it is presented the class of quaternary linear codes LRM(r,m) whose images under the Gray map are binary codes with parameters of Reed-Muller RM(r,m) code of order r.

In a DNA sequence, we have the celebrated Watson-Crick complement $\overline{T}=A$, $\overline{A}=T$, $\overline{C}=G$, and $\overline{G}=C$. Given an integer $m\ge 2$, a secondary structure in a DNA sequence refers to the existence of two…

In this paper, we introduce a new definitions of the Gray weight and the Gray map for linear codes over $\mathbb{Z}_9+u\mathbb{Z}_9$ with $u^2=u$. Some results on self-dual codes over this ring are investigated. Further, the structural…