Related papers: Codes in the Damerau Distance for DNA Storage
We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…
A set of linearly constrained permutation matrices are proposed for constructing a class of permutation codes. Making use of linear constraints imposed on the permutation matrices, we can formulate a minimum Euclidian distance decoding…
Constrained codes are used to prevent errors from occurring in various data storage and data transmission systems. They can help in increasing the storage density of magnetic storage devices, in managing the lifetime of electronic storage…
The coverage depth problem in DNA data storage is about minimizing the expected number of reads until all data is recovered. When they exist, MDS codes offer the best performance in this context. This paper focuses on the scenario where the…
The edit distance under the DCJ model can be computed in linear time for genomes with equal content or with Indels. But it becomes NP-Hard in the presence of duplications, a problem largely unsolved especially when Indels are considered. In…
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…
Synthetic polymer-based storage seems to be a particularly promising candidate that could help to cope with the ever-increasing demand for archival storage requirements. It involves designing molecules of distinct masses to represent the…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for both unique string…
This manuscript is an extended abstract version of the paper entitled ``Quantum Deletion Codes derived from Classical Deletion Codes.'' The paper contributes to the fundamental theory for quantum deletion error-correcting codes. The paper…
The increasing demand for data storage has prompted the exploration of new techniques, with molecular data storage being a promising alternative. In this work, we develop coding schemes for a new storage paradigm that can be represented as…
A basic problem for the constant dimension subspace coding is to determine the maximal possible size A_q (n, d, k) of a set of k-dimensional subspaces in Fnq such that the subspace distance satisfies d(U, V )> or =d for any two different…
Large-scale distributed storage systems typically use erasure codes to provide durability of data in the face of failures. A set of $k$ blocks to be stored is encoded using an $[n, k]$ code to generate $n$ blocks that are then stored on…
In this paper, we consider a concatenated coding based class of DNA storage codes in which the selected molecules are constrained to be taken from an ``inner'' codebook associated with the sequencing channel. This codebook is used in a…
Linear network coding transmits information in terms of a basis of a vector space and the information is received as a basis of a possible altered vectorspace. Ralf Koetter and Frank R. Kschischang in Coding for errors and erasures in…
We propose a novel coding scheme for DNA-based storage systems, called the shift-interleave (SI) coding, designed to correct insertion, deletion, and substitution (IDS) errors, as well as sequence losses. The SI coding scheme employs…
Motivated by applications to DNA storage, we study reconstruction and list-reconstruction schemes for integer vectors that suffer from limited-magnitude errors. We characterize the asymptotic size of the intersection of error balls in…
In this review paper, we delve into the nascent field of molecular data storage, focusing on system implementations and code constructions. We start by providing an overview of basic concepts in synthetic and computational biology.…
The minimum distance of a linear code is a key concept in information theory. Therefore, the time required by its computation is very important to many problems in this area. In this paper, we introduce a family of implementations of the…
In this work, multilayer crisscross error and erasures are considered, which affect entire rows and columns in the matrices of a list of matrices. To measure such errors and erasures, the multi-cover metric is introduced. Several bounds are…
We investigate the maximum cardinality and the mathematical structure of error-correcting codes endowed with the Kendall-$\tau$ metric. We establish an averaging bound for the cardinality of a code with prescribed minimum distance, discuss…