Related papers: Coding for Optimized Writing Rate in DNA Storage
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
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…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (rarely accessed data), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…
As a possible implementation of data storage using DNA, multiple strands of DNA are stored in a liquid container so that, in the future, they can be read by an array of DNA readers in parallel. These readers will sample the strands with…
Motivation: Next Generation Sequencing technologies revolutionized many fields in biology by enabling the fast and cheap sequencing of large amounts of genomic data. The ever increasing sequencing capacities enabled by current sequencing…
Proteins employ the information stored in the genetic code and translated into their sequences to carry out well-defined functions in the cellular environment. The possibility to encode for such functions is controlled by the balance…
Encoding information in combinations of pre-synthesised deoxyribonucleic acid (DNA) strands (referred to as motifs) is an interesting approach to DNA storage that could potentially circumvent the prohibitive costs of…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
When an individual's DNA is sequenced, sensitive medical information becomes available to the sequencing laboratory. A recently proposed way to hide an individual's genetic information is to mix in DNA samples of other individuals. We…
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…
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 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…
Biological data mainly comprises of Deoxyribonucleic acid (DNA) and protein sequences. These are the biomolecules which are present in all cells of human beings. Due to the self-replicating property of DNA, it is a key constitute of genetic…
As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…
The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS) errors, as well as sequence-level…
We present a finite blocklength performance bound for a DNA storage channel with insertions, deletions, and substitutions. The considered bound -- the dependency testing (DT) bound, introduced by Polyanskiy et al. in 2010 -- provides an…
With recent high-throughput technology we can synthesize large heterogeneous collections of DNA structures, and also read them all out precisely in a single procedure. Can we use these tools, not only to do things faster, but also to devise…
A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…