Related papers: DNA codes over two noncommutative rings of order f…
We introduce self-dual codes over the Kleinian four group $K = \mathbb{Z}_2 \times \mathbb{Z}_2$ for a natural quadratic form on $K^n$ and develop the theory. Topics studied are: weight enumerators, mass formulas, classification up to…
Motivated by applications in DNA storage, we study a setting in which strings are affected by tandem-duplication errors. In particular, we look at two settings: disjoint tandem-duplication errors, and equal-length tandem-duplication errors.…
Cyclicity of a convolutional code (CC) is relying on a nontrivial automorphism of the algebra F[x]/(x^n-1), where F is a finite field. If this automorphism itself has certain specific cyclicity properties one is lead to the class of…
Let $q$ be a power of a prime $p$. In this paper, we study reversible cyclic codes of arbitrary length over the ring $ R = \mathbb{F}_q + u \mathbb{F}_q$, where $u^2=0 mod q$. First, we find a unique set of generators for cyclic codes over…
Self-dual double circulant codes of odd dimension are shown to be dihedral in even characteristic and consta-dihedral in odd characteristic. Exact counting formulae are derived for them and used to show they contain families of codes with…
In this paper, we study the codes over the matrix ring over $\mathbb{Z}_4$, which is perhaps the first time the ring structure $M_2(\mathbb{Z}_4)$ is considered as a code alphabet. This ring is isomorphic to…
The study of constant-weight codes in $\ell_1$-metric was motivated by the duplication-correcting problem for data storage in live DNA. It is interesting to determine the maximum size of a code given the length $n$, weight $w$, minimum…
Classes of self-dual codes and dual-containing codes are constructed. The codes are obtained within group rings and, using an isomorphism between group rings and matrices, equivalent codes are obtained in matrix form. Distances and other…
Much evolutionary information is stored in the fluctuations of protein length distributions. The genome size and non-coding DNA content can be calculated based only on the protein length distributions. So there is intrinsic relationship…
In this paper, two new families of MDS quantum convolutional codes are constructed. The first one can be regarded as a generalization of \cite[Theorem 6.5]{GGGlinear}, in the sense that we do not assume that $q\equiv1\pmod{4}$. More…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
In this paper, we present several new constructions of differentially 4-uniform permutations over $\F_{2^{2m}}$ by modifying the values of the inverse function on some subsets of $\F_{2^{2m}}$. The resulted differentially 4-uniform…
The presence of low dimensional chaos in the protein secondary structures, using the binary coded $\alpha$-helices and $\beta$-sheet motifs, has been investigated. In order to analyse symbolic DNA/RNA sequences the assignment, based on the…
We discuss a class of binary cyclic codes and their dual codes. The minimum distance is determined using algebraic geometry, and an application of Weil's theorem. We relate the weights appearing in the dual codes to the number of rational…
In this paper, we investigate the existence and asymptotic property of self-dual $2$-quasi negacyclic codes of length $2n$ over a finite field of cardinality $q$. When $n$ is odd, we show that the $q$-ary self-dual $2$-quasi negacyclic…
The ring in the title is the first non commutative ring to have been used as alphabet for block codes. The original motivation was the construction of some quaternionic modular lattices from codes. The new application is the construction of…
One of the main objectives of quantum error-correction theory is to construct quantum codes with optimal parameters and properties. In this paper, we propose a class of 2-generator quasi-cyclic codes and study their applications in the…
In this paper, we investigate the structure and properties of additive complementary dual (ACD) codes over the mixed alphabet $\mathbb{F}_2\mathbb{F}_4$ relative to a certain inner product defined over $\mathbb{F}_2\mathbb{F}_4$. We…
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…
For $q$-ary $n$-sequences, we develop the concept of similarity functions that can be used (for $q=4$) to model a thermodynamic similarity on DNA sequences. A similarity function is identified by the length of a longest common subsequence…