Related papers: New Constructions of Reversible DNA Codes
Maximum-distance separable (MDS) convolutional codes are characterized by the property that their free distance reaches the generalized Singleton bound. In this paper, new criteria to construct MDS convolutional codes are presented.…
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,…
In this paper we construct constant dimension space codes with prescribed minimum distance. There is an increased interest in space codes since a paper by Koetter and Kschischang were they gave an application in network coding. There is…
It is an important task to construct quantum maximum-distance-separable (MDS) codes with good parameters. In the present paper, we provide six new classes of q-ary quantum MDS codes by using generalized Reed-Solomon (GRS) codes and…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
Constant dimension codes are e.g. used for error correction and detection in random linear network coding, so that constructions for these codes have achieved wide attention. Here, we improve over 150 lower bounds by describing better…
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…
A method for encoding information in DNA sequences is described. The method is based on the precision-resolution framework, and is aimed to work in conjunction with a recently suggested terminator-free template independent DNA synthesis…
Upper bounds on the maximum number of codewords in a binary code of a given length and minimum Hamming distance are considered. New bounds are derived by a combination of linear programming and counting arguments. Some of these bounds…
By employing the residue polynomials, a construction of constant-composition codes is given. This construction generalizes the one proposed by Xing[16]. It turns out that when d=3 this construction gives a lower bound of…
DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on…
We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing…
Secure codes are widely-studied combinatorial structures which were introduced for traitor tracing in broadcast encryption. To determine the maximum size of such structures is the main research objective. In this paper, we investigate the…
Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
A genetic algorithm is suitable for exploring large search spaces as it finds an approximate solution. Because of this advantage, genetic algorithm is effective in exploring vast and unknown space such as molecular search space. Though the…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
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…
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 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…