24 papers · ranked by Valyu relevance
Ian Holmes
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 interleaving watermark and periodic marker signals; conversion from binary to…
David Haughton, Félix Balado
Background In recent times, the application of deoxyribonucleic acid (DNA) has diversified with the emergence of fields such as DNA computing and DNA data embedding. DNA data embedding, also known as DNA watermarking or DNA steganography, aims to develop robust algorithms for encoding non-genetic information in DNA.…
Paridhi Latawa, Nuh Aydın
| 1 | Abstract | | 2 | | --- | --- | --- | --- | | 2 | | Introduction | 2 | | 3 | | Convolutional Codes | 3 | | | 3.1 | Encoding of Binary Convolutional Codes | 3 | | | 3.2 | Decoding Convolutional Codes | 11 | | | 3.3 | Truncated Viterbi Decoding | 13 | | 4 | | DNA Codes | 17 | | | 4.1 | Constraints for the…
G. Nallappa Bhavithran, R. Selvakumar
The biggest challenge when using DNA as a storage medium is maintaining its stability. The relative occurrence of Guanine (G) and Cytosine (C) is essential for the longevity of DNA. In addition to that, reverse complementary base pairs should not be present in the code. These challenges are overcome by a proper choice…
Pavani Yashodha De Silva, Gamage Upeksha Ganegoda
With the exponential growth in the capacity of information generated and the emerging need for data to be stored for prolonged period of time, there emerges a need for a storage medium with high capacity, high storage density, and possibility to withstand extreme environmental conditions. DNA emerges as the prospective…
Dixita Limbachiya, Bansari Rao, Manish K. Gupta
The idea of computing with DNA was given by Tom Head in 1987, however in 1994 in a seminal paper, the actual successful experiment for DNA computing was performed by Adleman. The heart of the DNA computing is the DNA hybridization, however, it is also the source of errors. Thus the success of the DNA computing depends…
Krishna Gopal Benerjee, Sourav Deb, Manish Gupta
—DNA storage has emerged as an important area of research. The reliability of DNA storage system depends o n designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a special constraint. Each codeword of the DNA code has a specific property that…
Ian Holmes
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 interleaving watermark and periodic marker signals; conversion from binary to…
Zhi Ping, Dongzhao Ma, Xiaoluo Huang, Shihong Chen + 4 more
'Fei Guo' 'Sha Joe Zhu' 'Yue Shen'] Title: Abstract The information explosion has led to a rapid increase in the amount of data requiring physical storage. However, in the near future, existing storage methods (i.e., magnetic and optical media) will be insufficient to store these exponentially growing data. Therefore…
Zhi Ping, Haoling Zhang, Shihong Chen, Qianlong Zhuang + 2 more
Chamaeleo is currently the only collection library that focuses on adapting multiple well-established coding schemes for DNA storage. It provides a tool for researchers to study various coding schemes and apply them in practice. Chamaeleo adheres to the concept of high aggregation and low coupling for software design…
Dan Tulpan, Chaouki Regoui, Guillaume Durand, Luc Belliveau + 1 more
'Serge Léger'] This paper presents a novel hybrid DNA encryption (HyDEn) approach that uses randomized assignments of unique error-correcting DNA Hamming code words for single characters in the extended ASCII set. HyDEn relies on custom-built quaternary codes and a private key used in the randomized assignment of code…
Thomas Heinis, Roman Sokolovskii, Jamie J. Alnasir
Key to DNA storage is encoding the information to a sequence of nucleotides before it can be synthesised for storage. Definition of such an encoding or mapping must adhere to multiple design restrictions. First, not all possible sequences of nucleotides can be synthesised. Homopolymers, e.g., sequences of the same…
Azat Akhmetov, Andrew D. Ellington, Edward M. Marcotte
Background Encoding arbitrary digital information in DNA has attracted attention as a potential avenue for large scale and long term data storage. However, in order to enable DNA data storage technologies there needs to be improvements in data storage fidelity (tolerance to mutation), the facility of writing and…
Zihui Yan, Haoran Zhang, Boyuan Lu, Tong Han + 2 more
'Yingjin Yuan'] Title: ABSTRACT The long-term preservation of large volumes of infrequently accessed cold data poses challenges to the storage community. Deoxyribonucleic acid (DNA) is considered a promising solution due to its inherent physical stability and significant storage density. The information density and…
Penghao Wang, Ziniu Mu, Lijun Sun, Shuqing Si + 1 more
DNA is a natural storage medium with the advantages of high storage density and long service life compared with traditional media. DNA storage can meet the current storage requirements for massive data. Owing to the limitations of the DNA storage technology, the data need to be converted into short DNA sequences for…
Andreas L. Gimpel, Alex Remschak, Wendelin J. Stark, Reinhard Heckel + 1 more
A wide range of codecs with vastly different error-correction approaches have been proposed and implemented for DNA data storage to date. However, while many codecs claim to provide superior performance, no studies have systematically benchmarked codec implementations to establish the current state-of-the-art in DNA…
Xiaoluo Huang, Yu Wang, Jiaxin Xu, Ziang Nie + 5 more
DNA data storage offers a viable strategy to address the impending data explosion. Early attempts to harness DNA as a storage medium have encountered scalability limitations, largely due to the complexity of codec algorithms, the generation of biochemically harmful sequences and lack of a robust architecture. We…
Inbal Preuss, Michael Rosenberg, Zohar Yakhini, Leon Anavy
With the world generating digital data at an exponential rate, DNA has emerged as a promising archival medium. It offers a more efficient and long-lasting digital storage solution due to its durability, physical density, and high information capacity. Research in the field includes the development of encoding schemes…
HANIYEH ABDOLLAHZADEH, Tonya Peeples, Mohammad Shahcheraghi
DNA-based nanomaterials have shown great potential in numerous applications, thanks to their unique properties including DNA's various molecular interactions, programmability, and versatility with biological modules. Meanwhile, the DNA origami platforms have shown promise in the creation of drug carriers. This…
Ibrahim Nawaz, Parv Agarwal, Thomas Heinis
DNA storage is a developing field that uses DNA to archive digital data owing to its superior information density and stability. Although DNA storage has been performed on a significant scale, challenges arise from the synthesis and sequencing of data-encoded oligonucleotides. Synthesis of DNA introduces significant…
Miloje Rakočević
In some previous works (2018a,b; 2019, 2021a,b, 2022) we presented a new type of mirror symmetry, expressed in the set of protein amino acids; such a symmetry, that it simultaneously represents the semiotic essence of the genetic code. In this paper we provide new evidences that the genetic code represents the unity of…
Benjamin King, Max Winokan, Paul Stevenson, Jim Al-Khalili + 2 more
The adenine-thymine tautomer (A-T) has previously been discounted as a spontaneous mutagenesis mechanism due to the energetic instability of the tautomeric configuration. We study the stability of A-T while the nucleobases undergo DNA strand separation. Our calculations indicate an increase in the stability of A-T as…
Tanay Debnath, G. Andres Cisneros
Incorporation of artificial 3rd base pairs (Unnatural base pairs, UBPs) has emerged as a fundamental technique in pursuit of expanding the genetic alphabet. 2,6-dimethyl-2H-isoquiniline-1-thione: D5SIC (DS) and 2-methoxy-3-methylnaphthalene: DNAM (DN), a potential unnatural base pair (UBP) developed by Romesberg and…
Babu Bassa
In this communication the author describes a software tool named "ChameleonSort". The software program, developed by the present author is useful in the sorting of biological sequence variants like those accumulating mutations while diverging from the common ancestors. Examples include viral protein variants, protein…