相关论文: Bounds for DNA codes with constant GC-content
We consider the problem of designing optimal linear codes (in terms of having the largest minimum distance) subject to a support constraint on the generator matrix. We show that the largest minimum distance can be achieved by a subcode of a…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
We design a heuristic method, a genetic algorithm, for the computation of an upper bound of the minimum distance of a linear code over a finite field. By the use of the row reduced echelon form, we obtain a permutation encoding of the…
While achieving a compression ratio of 2.0 bits/base, the new algorithm codes non-N bases in fixed length. It dramatically reduces the time of coding and decoding than previous DNA compression algorithms and some universal compression…
We study constacyclic codes, of length $np^s$ and $2np^s$, that are generated by the polynomials $(x^n + \gamma)^{\ell}$ and $(x^n - \xi)^i(x^n + \xi)^j$\ respectively, where $x^n + \gamma$, $x^n - \xi$ and $x^n + \xi$ are irreducible over…
We consider locally recoverable codes (LRCs) and aim to determine the smallest possible length $n=n_q(k,d,r)$ of a linear $[n,k,d]_q$-code with locality $r$. For $k\le 7$ we exactly determine all values of $n_2(k,d,2)$ and for $k\le 6$ we…
For $n,d,w \in \mathbb{N}$, let $A(n,d,w)$ denote the maximum size of a binary code of word length $n$, minimum distance $d$ and constant weight $w$. Schrijver recently showed using semidefinite programming that $A(23,8,11)=1288$, and the…
Let $A(n,d,w)$ be the largest possible size of an $(n,d,w)$ constant-weight binary code. By adding new constraints to Delsarte linear programming, we obtain twenty three new upper bounds on $A(n,d,w)$ for $n \leq 28$. The used techniques…
We study the upper bounds for $A(n,d)$, the maximum size of codewords with length $n$ and Hamming distance at least $d$. Schrijver studied the Terwilliger algebra of the Hamming scheme and proposed a semidefinite program to bound $A(n, d)$.…
Motivated by the duplication-correcting problem for data storage in live DNA, we study the construction of constant-weight codes in $\ell_1$-metric. By using packings and group divisible designs in combinatorial design theory, we give…
A method to construct and count all the linear codes (of arbitrary length) in $\mathbb{F}_{4}$ that are invariant under reverse permutation and that contain the repetition code is presented. These codes are suitable for constructing DNA…
The Gap-Hamming distance problem is the promise problem of deciding if the Hamming distance $h$ between two strings of length $n$ is greater than $a$ or less than $b$, where the gap $g=|a-b|\geq 1$ and $a$ and $b$ could depend on $n$. In…
This paper provides new constructive lower bounds for constant dimension codes, using different techniques such as Ferrers diagram rank metric codes and pending blocks. Constructions for two families of parameters of constant dimension…
New bounds on the cardinality of permutation codes equipped with the Ulam distance are presented. First, an integer-programming upper bound is derived, which improves on the Singleton-type upper bound in the literature for some lengths.…
Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of…
We give a new asymptotic upper bound on the size of a code in the Grassmannian space. The bound is better than the upper bounds known previously in the entire range of distances except very large values.
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…
Convolutional codes with a maximum distance profile attain the largest possible column distances for the maximum number of time instants and thus have outstanding error-correcting capability especially for streaming applications. Explicit…
This paper extends the foundational work of Dollma \emph{et al}. on codes for ordered composite DNA sequences. We consider the general setting with an alphabet of size $q$ and a resolution parameter $k$, moving beyond the binary ($q=2$)…
In this work we investigate unions of lifted MRD codes of a fixed dimension and minimum distance and derive an explicit formula for the cardinality of such codes. This will then imply a lower bound on the cardinality of constant dimension…