2D Graphical Representation of DNA Sequences Based on Variant Map

Wu, Ruoxue; Liu, Wenjia; Mao, Yong; Zheng, Jeffrey

doi:10.1109/access.2020.3025591

Cited by 5 publications

(4 citation statements)

References 30 publications

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“…Table 7 illustrates a list of evaluation metrics along with its definition and abbreviation 65 – 70 .…”

Section: Evaluation Metricsmentioning

confidence: 99%

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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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“…Table 7 illustrates a list of evaluation metrics along with its definition and abbreviation 65 – 70 .…”

Section: Evaluation Metricsmentioning

confidence: 99%

“…Table 7 illustrates a list of evaluation metrics along with its definition and abbreviation [65][66][67][68][69][70] . Table 8 illustrates a summarized view of used evaluation metrics in various research studies.…”

Section: Evaluation Metricsmentioning

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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show abstract

“…The 2D graphic representation of the DNA sequence proposed by Liu is based on the horizon lines [30]. Another 2D graphical representation of DNA sequences proposed by Wu et al is based on variant map [31]. The goal is to create approaches in which both graphs and numerical characteristics, often referred to as sequence descriptors, represent a biological sequence in a unique (i.e., degeneracy-free) way.…”

Section: G G T T G G a A 2 G T G T G A G Amentioning

confidence: 99%

4D-Dynamic Representation of DNA/RNA Sequences: Studies on Genetic Diversity of Echinococcus multilocularis in Red Foxes in Poland

Bielińska-Wąż

Wąż

Lass

et al. 2022

Life

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The 4D-Dynamic Representation of DNA/RNA Sequences, an alignment-free bioinformatics method recently developed by us, has been used to study the genetic diversity of Echinococcus multilocularis in red foxes in Poland. Sequences of three mitochondrial genes, i.e., NADH dehydrogenase subunit 2 (nad2), cytochrome b (cob), and cytochrome c oxidase subunit 1 (cox1), are analyzed. The sequences are represented by sets of material points in a 4D space, i.e., 4D-dynamic graphs. As a visualization of the sequences, projections of the graphs into 3D space are shown. The differences between 3D graphs corresponding to European, Asian, and American haplotypes are small. Numerical characteristics (sequence descriptors) applied in the studies can recognize the differences. The concept of creating descriptors of 4D-dynamic graphs has been borrowed from classical dynamics; these are coordinates of the centers or mass and moments of inertia of 4D-dynamic graphs. Based on these descriptors, classification maps are constructed. The concentrations of points in the maps indicate one Polish haplotype (EmPL9) of Asian origin.

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“…Similarity studies of the sequences using graphical techniques are commonly used approaches. Each method reveals different aspects of similarity and still new approaches are being constructed in bioinformatics [61][62][63][64][65][66][67][68][69][70][71]. For example, we created Spectral-Dynamic Representation of DNA Sequences [65] or 4D-Dynamic Representation of DNA/RNA Sequences and applied this bioinformatics method to studies on the origin of the SARS-CoV-2 virus [60].…”

Section: Introductionmentioning

confidence: 99%

Classification Maps: A New Mathematical Tool Supporting the Diagnosis of Age-Related Macular Degeneration

Wąż

Zorena

Murawska

et al. 2023

JPM

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Objective: A new diagnostic graphical tool—classification maps—supporting the detection of Age-Related Macular Degeneration (AMD) has been constructed. Methods: The classification maps are constructed using the ordinal regression model. In the ordinal regression model, the ordinal variable (the dependent variable) is the degree of the advancement of AMD. The other variables, such as CRT (Central Retinal Thickness), GCC (Ganglion Cell Complex), MPOD (Macular Pigment Optical Density), ETDRS (Early Treatment Diabetic Retinopathy Study), Snellen and Age have also been used in the analysis and are represented on the axes of the maps. Results: Here, 132 eyes were examined and classified to the AMD advancement level according to the four-point Age-Related Eye Disease Scale (AREDS): AREDS 1, AREDS 2, AREDS 3 and AREDS 4. These data were used for the creation of two-dimensional classification maps for each of the four stages of AMD. Conclusions: The maps allow us to perform the classification of the patient’s eyes to particular stages of AMD. The pairs of the variables represented on the axes of the maps can be treated as diagnostic identifiers necessary for the classification to particular stages of AMD.

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2D Graphical Representation of DNA Sequences Based on Variant Map

Cited by 5 publications

References 30 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

4D-Dynamic Representation of DNA/RNA Sequences: Studies on Genetic Diversity of Echinococcus multilocularis in Red Foxes in Poland

Classification Maps: A New Mathematical Tool Supporting the Diagnosis of Age-Related Macular Degeneration

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