Related papers: DNA codes from $(\text{\textbaro}, \mathfrak{d}, \…
In DNA-based data storage, DNA codes with biochemical constraints and error correction are designed to protect data reliability. Single-stranded DNA sequences with secondary structure avoidance (SSA) help to avoid undesirable secondary…
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
In this paper we investigate the class of constacyclic codes, which is a natural generalization of the class of cyclic and negacyclic codes. This class of codes is interesting in the sense that it contains codes with good or even optimal…
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…
Codes over Galois rings have been studied extensively during the last three decades. Negacyclic codes over $GR(2^a,m)$ of length $2^s$ have been characterized: the ring $\mathcal{R}_2(a,m,-1)= \frac{GR(2^a,m)[x]}{\langle x^{2^s}+1\rangle}$…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
Let $R=\mathbb{F}_2+u\mathbb{F}_2+u^2\mathbb{F}_2$ be a non-chain finite commutative ring, where $u^3=u$. In this paper, we mainly study the construction of quantum codes from cyclic codes over $R$. We obtained self-orthogonal codes over…
This paper considers cyclic DNA codes of arbitrary length over the ring $R=\F_2[u]/u^4-1$. A mapping is given between the elements of $R$ and the alphabet $\{A,C,G,T\}$ which allows the additive stem distance to be extended to this ring.…
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…
This work concerns formal descriptions of DNA code properties, and builds on previous work on transducer descriptions of classic code properties and on trajectory descriptions of DNA code properties. This line of research allows us to give…
Coterm polynomials are introduced by Oztas et al. [a novel approach for constructing reversible codes and applications to DNA codes over the ring $F_2[u]/(u^{2k}-1)$, Finite Fields and Their Applications 46 (2017).pp. 217-234.], which…
We derive theoretical upper and lower bounds on the maximum size of DNA codes of length n with constant GC-content w and minimum Hamming distance d, both with and without the additional constraint that the minimum Hamming distance between…
New families of unit memory as well as multi-memory convolutional codes are constructed algebraically in this paper. These convolutional codes are derived from the class of group character codes. The proposed codes have basic generator…
In this paper, we determine depth spectra of all repeated-root $(\alpha+\gamma \beta)$-constacyclic codes of arbitrary lengths over a finite commutative chain ring $\mathcal{R},$ where $\alpha$ is a non-zero element of the Teichm\"{u}ller…
In this paper, we have studied cyclic codes over the ring $R=\mathbb{Z}_4+u\mathbb{Z}_4$, $u^2=0$. We have considered cyclic codes of odd lengths. A sufficient condition for a cyclic code over $R$ to be a $\mathbb{Z}_4$-free module is…
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…
Let $\mathbb{F}_{p^{m}}$ be a finite field with cardinality $p^{m}$ and $R=\mathbb{F}_{p^{m}}+u\mathbb{F}_{p^{m}}$ with $u^{2}=0$. We aim to determine all $\alpha+u\beta$-constacyclic codes of length $np^{s}$ over $R$, where…
We first define a new Gray map from $R=\mathbb{Z}_4+u\mathbb{Z}_4$ to $\mathbb{Z}^{2}_{4}$, where $u^2=1$ and study $(1+2u)$-constacyclic codes over $R$. Also of interest are some properties of $(1+2u)$-constacyclic codes over $R$.…