Encoding scheme for data storage and retrieval on DNA computers

Sharma, Dolly; Kumar, Ranjit; Gupta, Mayuri; Saxena, Tanisha

doi:10.1049/iet-nbt.2020.0157

Cited by 4 publications

(6 citation statements)

References 47 publications

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“…Eungi Hong presented a color image cryptosystem using dynamic DNA encryption and a four-wing hyper chaotic system 35 . Mousomi Roy worked with dynamic DNA encoding and asymmetric cryptosystems for data secrecy 45 . Wei Feng used a DNA-based fuzzy vault scheme to protect IIoT device keys.…”

Section: Related Work On the Dna Encoding Schemementioning

confidence: 99%

DNA encoding schemes herald a new age in cybersecurity for safeguarding digital assets

Aqeel,

Khan,

Khan

et al. 2024

Sci Rep

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With the urge to secure and protect digital assets, there is a need to emphasize the immediacy of taking measures to ensure robust security due to the enhancement of cyber security. Different advanced methods, like encryption schemes, are vulnerable to putting constraints on attacks. To encode the digital data and utilize the unique properties of DNA, like stability and durability, synthetic DNA sequences are offered as a promising alternative by DNA encoding schemes. This study enlightens the exploration of DNA’s potential for encoding in evolving cyber security. Based on the systematic literature review, this paper provides a discussion on the challenges, pros, and directions for future work. We analyzed the current trends and new innovations in methodology, security attacks, the implementation of tools, and different metrics to measure. Various tools, such as Mathematica, MATLAB, NIST test suite, and Coludsim, were employed to evaluate the performance of the proposed method and obtain results. By identifying the strengths and limitations of proposed methods, the study highlights research challenges and offers future scope for investigation.

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Section: Related Work On the Dna Encoding Schemementioning

confidence: 99%

DNA encoding schemes herald a new age in cybersecurity for safeguarding digital assets

Aqeel,

Khan,

Khan

et al. 2024

Sci Rep

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“…Spatial arrangement of DNA sequence depends on many physicochemical factors, like ionic interaction, hydrogen bonding, base stacking, pH, salt concentration, superposing, etc. [ 6 ]. Although all physicochemical properties are important, hydrogen bonding, stacking, and solvation based energies play critical roles in maintaining the structural integrity of DNA molecules [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

“…[6]. Although all physicochemical properties are important, hydrogen bonding, stacking, and solvation based energies play critical roles in maintaining the structural integrity of DNA molecules[7].…”

mentioning

confidence: 99%

Composition, physicochemical property and base periodicity for discriminating lncRNA and mRNA

Krishnamachari

2023

Bioinformation

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Annotation of genome data with biological features is a challenging problem. One such problem deals with distinguishing lncRNA from mRNA. In this study, three groups of classification features, namely base periodicity, physicochemical property and nucleotide compositions were considered. We are attempting to propose a simple neural network model to obtain better results using judicious combination of the above said sequence features. Our approach uses balanced dataset, simple prediction model and use of limited features in distinguishing lncRNA and mRNA. Accordingly (a) two properties of base periodicity: peak power spectrum of the signal and noise-to-signal ratio (SNR) of this peak signal (b) three physicochemical properties: solvation, stacking and hydrogen-bonding energy and (c) all dinucleotides and trinucleotides compositions were used. Classification was performed by considering features independently followed by combining these properties for improvement. Classification metric was used to compare the result for seven eukaryotic organisms for various combinations of features. Nucleotide compositions combined with physicochemical property or base periodicity group of features becomes a strong classifier with more than 99 percentage accuracy. Base periodicity analysis with SNR can be used as discriminating feature of lncRNA from mRNA.

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“…[ 15 ] Therefore, encoding systems including different functional modules, such as index design and error correction, are required to accommodate the characteristics of the DNA storage channel: i) DNA sequences with acceptable synthetic errors are generally limited to about 250 nucleotides and large data is thus divided into short DNA sequences. Therefore, redundant nucleotides are required to index the DNA sequences for data reconstruction [ 13,16 ] and redundant sequences are required for error correction caused by DNA sequence losses. ii) The existence of homopolymers with repeating bases ≥3 and inappropriate GC contents may increase the error rate in DNA sequencing.…”

Section: Introductionmentioning

confidence: 99%

“…The unmet need between exponentially increasing data and limited capacity of current mainstream storage media is becoming increasingly prominent. [1][2][3] Traditional storage media, such as magnetic, optical, and solid-state media, only index the DNA sequences for data reconstruction [13,16] and redundant sequences are required for error correction caused by DNA sequence losses. ii) The existence of homopolymers with repeating bases ≥3 and inappropriate GC contents may increase the error rate in DNA sequencing.…”

Section: Introductionmentioning

confidence: 99%

DNA‐Based Concatenated Encoding System for High‐Reliability and High‐Density Data Storage

et al. 2022

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possess binary coding of "1" or "0" on each bit, and their storage capacity is about to reach its maximum. Thus, it is urgent to develop novel storage media with lowpower consumption, high storage density, and long lifespan. Deoxyribonucleic acid (DNA), known as the genetic information carrier, [4,5] has proved to be a promising data storage medium due to its long lifespan, [6][7][8][9][10] sky-high storage density, low energy consumption, and low maintenance cost. [11][12][13] Natural DNA has four nucleotides (A, T, C, and G) and has a storage density of ≈460 EB g −1 , [14] which is much higher than that of traditional storage media. Therefore, the development of new types of DNA molecules to improve information storage is an attractive goal.DNA data storage is mainly affected by the number of nucleotides, the biochemical properties of DNA, and the technical constraints of DNA synthesis and sequencing. [15] Therefore, encoding systems including different functional modules, such as index design and error correction, are required to accommodate the characteristics of the DNA storage channel: i) DNA sequences with acceptable synthetic errors are generally limited to about 250 nucleotides and large data is thus divided into short DNA sequences. Therefore, redundant nucleotides are required to Information storage based on DNA molecules provides a promising solution with advantages of low-energy consumption, high storage efficiency, and long lifespan. However, there are only four natural nucleotides and DNA storage is thus limited by 2 bits per nucleotide. Here, artificial nucleotides into DNA data storage to achieve higher coding efficiency than 2 bits per nucleotide is introduced. To accommodate the characteristics of DNA synthesis and sequencing, two high-reliability encoding systems suitable for four, six, and eight nucleotides, i.e., the RaptorQ-Arithmetic-LZW-RS (RALR) and RaptorQ-Arithmetic-Base64-RS (RABR) systems, are developed. The two concatenated encoding systems realize the advantages of correcting DNA sequence losses, correcting errors within DNA sequences, reducing homopolymers, and controlling specific nucleotide contents. The average coding efficiencies with error correction and without arithmetic compression by the RALR system using four, six, and eight nucleotides reach 1.27, 1.61, and 1.85 bits per nucleotide, respectively. While the average coding efficiencies by the RABR system are up to 1.50, 2.00, and 2.35 bits per nucleotide, respectively. The coding efficiency, versatility, and tunability of the developed artificial DNA systems might provide significant guidance for high-reliability and high-density data storage.

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Encoding scheme for data storage and retrieval on DNA computers

Cited by 4 publications

References 47 publications

DNA encoding schemes herald a new age in cybersecurity for safeguarding digital assets

DNA encoding schemes herald a new age in cybersecurity for safeguarding digital assets

Composition, physicochemical property and base periodicity for discriminating lncRNA and mRNA

DNA‐Based Concatenated Encoding System for High‐Reliability and High‐Density Data Storage

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