Related papers: GC+ Code: A Systematic Short Blocklength Code for …
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…
The efficient storage of digital data is becoming very challenging over the years due to the exponential increase in the generation of data which can't compete with the existing storage resources. Furthermore, the infrequently accessed data…
We consider the problem of storing and retrieving information from synthetic DNA media. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on their collection of substrings…
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…
Erasure correcting codes are widely used to ensure data persistence in distributed storage systems. This paper addresses the simultaneous repair of multiple failures in such codes. We go beyond existing work (i.e., regenerating codes by…
In the recent years, DNA has emerged as a potentially viable storage technology. DNA synthesis, which refers to the task of writing the data into DNA, is perhaps the most costly part of existing storage systems. Accordingly, this high cost…
This work presents a theoretical analysis of the probability of successfully retrieving data encoded with MDS codes (e.g., Reed-Solomon codes) in DNA storage systems. We study this probability under independent and identically distributed…
DNA exhibits remarkable potential as a data storage solution due to its impressive storage density and long-term stability, stemming from its inherent biomolecular structure. However, developing this novel medium comes with its own set of…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
The design of large libraries of oligonucleotides having constant GC-content and satisfying Hamming distance constraints between oligonucleotides and their Watson-Crick complements is important in reducing hybridization errors in DNA…
An indel refers to a single insertion or deletion, while an edit refers to a single insertion, deletion or substitution. In this paper, we investigate codes that combat either a single indel or a single edit and provide linear-time…
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…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
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…
We propose a novel and flexible DNA-storage architecture, which divides the storage space into fixed-size units (blocks) that can be independently and efficiently accessed at random for both read and write operations, and further allows…
This paper presents our computational methodology using Genetic Algorithms (GA) for exploring the nature of RNA editing. These models are constructed using several genetic editing characteristics that are gleaned from the RNA editing system…
This study explores the self-synchronization problem in DNA coding, specifically addressing single-deletion errors without using delimiters between codewords. We aim to identify the beginning of each codeword without using delimiters,…
Regenerating codes are a class of codes proposed for providing reliability of data and efficient repair of failed nodes in distributed storage systems. In this paper, we address the fundamental problem of handling errors and erasures during…
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…
Motivated by DNA-based data storage, we investigate a system where digital information is stored in an unordered set of several vectors over a finite alphabet. Each vector begins with a unique index that represents its position in the whole…