Related papers: On reversible and reversible-complementary DNA cod…
We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called…
In the present paper we study the structure of cyclic DNA codes of even lenght over the ring $\mathbb{F}_2+u\mathbb{F}_2+u^2\mathbb{F}_2$ where $u^3=0$. We investigate two presentations of cyclic codes of even lenght over…
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…
Finding the minimum distance of linear codes is an NP-hard problem. Traditionally, this computation has been addressed by means of the design of algorithms that find, by a clever exhaustive search, a linear combination of some generating…
In this paper, we mainly study the some structure of cyclic DNA codes of odd length over the ring $R = \F_2[u,v]/\langle u^2-1,v^3-v,uv-vu \rangle$ which play an important role in DNA computing. We established a direct link between the…
In this study we determine the structure of reversible DNA codes obtained from skew cyclic codes. We show that the generators of such DNA codes enjoy some special properties. We study the structural properties of such family of codes and we…
Motivated by DNA storage in living organisms, and by known biological mutation processes, we study the reverse-complement string-duplication system. We fully classify the conditions under which the system has full expressiveness, for all…
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…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
Consider a binary word being transmitted through a communication channel that introduces deletable errors where each bit of the word is either retained, flipped, erased or deleted. The simplest code for correcting \emph{all} possible…
In this work, we study the DNA codes from the ring R = Z4 + wZ4, where w^2 = 2+2w with 16 elements. We establish a one to one correspondence between the elements of the ring R and all the DNA codewords of length 2 by defining a…
Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…
We give a recursive construction for projective Reed-Muller codes in terms of affine Reed-Muller codes and projective Reed-Muller codes in fewer variables. From this construction, we obtain the dimension of the subfield subcodes of…
Motivated by average-case trace reconstruction and coding for portable DNA-based storage systems, we initiate the study of \emph{coded trace reconstruction}, the design and analysis of high-rate efficiently encodable codes that can be…
Let $\mathscr{R}_{e,m}$ denote a finite commutative chain ring of even characteristic with maximal ideal $\langle u \rangle$ of nilpotency index $e \geq 3,$ Teichm$\ddot{u}$ller set $\mathcal{T}_{m},$ and residue field…
This paper considers a new alphabet set, which is a ring that we call $\mathbb{F}_4R$, to construct linear error-control codes. Skew cyclic codes over the ring are then investigated in details. We define a nondegenerate inner product and…
We derive the coding capacity for duplication-correcting codes capable of correcting any number of duplications. We do so both for reverse-complement duplications, as well as palindromic (reverse) duplications. We show that except for…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
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…
The use of permutation polynomials has appeared, along to their compositional inverses, as a good choice in the implementation of cryptographic systems. Hence, there has been a demand for constructions of these polynomials which…