Related papers: Coding for Ordered Composite DNA Sequences
This paper considers the problem of distributed source coding for a large network. A major obstacle that poses an existential threat to practical deployment of conventional approaches to distributed coding is the exponential growth of the…
One of the primary sequencing methods gaining prominence in DNA storage is nanopore sequencing, attributed to various factors. In this work, we consider a simplified model of the sequencer, characterized as a channel. This channel takes a…
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…
Compound channel models offer a simple and straightforward way of analyzing the stability of decoder design under model variations. With this work we provide a coding theorem for a large class of practically relevant compound channel…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…
We present a Compression Tool, "GenBit Compress", for genetic sequences based on our new proposed "GenBit Compress Algorithm". Our Tool achieves the best compression ratios for Entire Genome (DNA sequences) . Significantly better…
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…
We introduce a novel method to analyse complete genomes and recognise some distinctive features by means of an adaptive compression algorithm, which is not DNA-oriented. We study the Information Content as a function of the number of…
DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…
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…
DNA based storage systems received attention by many researchers. This includes archival and re-writable random access DNA based storage systems. In this work, we have developed an efficient technique to encode the data into DNA sequence by…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
Constrained sequence codes have been widely used in modern communication and data storage systems. Sequences encoded with constrained sequence codes satisfy constraints imposed by the physical channel, hence enabling efficient and reliable…
Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…
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…
We consider a molecular channel, in which messages are encoded to the frequency of objects in a pool, and whose output during reading time is a noisy version of the input frequencies, as obtained by sampling with replacement from the pool.…
To equip DNA-based data storage with random-access capabilities, Yazdi et al. (2018) prepended DNA strands with specially chosen address sequences called primers and provided certain design criteria for these primers. We provide explicit…
A (tandem) duplication of length $ k $ is an insertion of an exact copy of a substring of length $ k $ next to its original position. This and related types of impairments are of relevance in modeling communication in the presence of…
The main obstacles for the practical deployment of DNA-based data storage platforms are the prohibitively high cost of synthetic DNA and the large number of errors introduced during synthesis. In particular, synthetic DNA products contain…
In modern age, the increasing complexity of computation and communication technology is leading us towards the necessity of new paradigm. As a result, unconventional approach like DNA coding theory is gaining considerable attention. The…