ArticleJournal of theoretical biology2011
Three 3D graphical representations of DNA primary sequences based on the classifications of DNA bases and their applications.
Article in Journal of theoretical biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Improved Visualization Method of DNA Sequences and its Application in Phylogenetic Analysis.Combinatorial chemistry & high throughput screening · 2026Article
- Overview and Prospects of DNA Sequence Visualization.International journal of molecular sciences · 2025Review
- Visualization Methods for DNA Sequences: A Review and Prospects.Biomolecules · 2024Review
- Polarization- and Chaos-Game-Based Fingerprinting of Molecular Targets of Listeria Monocytogenes Vaccine and Fully Virulent Strains.Current issues in molecular biology · 2023Article
- Bioinformatics tools for the sequence complexity estimates.Biophysical reviews · 2023Review
- Quantification of the Diversity in Gene Structures Using the Principles of Polarization Mapping.Current issues in molecular biology · 2023Article
- Alignment-free genomic sequence comparison using FCGR and signal processing.BMC bioinformatics · 2019Article
- Similarity Estimation Between DNA Sequences Based on Local Pattern Histograms of Binary Images.Genomics, proteomics & bioinformatics · 2016Article
- Circular Helix-Like Curve: An Effective Tool of Biological Sequence Analysis and Comparison.Computational and mathematical methods in medicine · 2016Article
- Sequence comparison via polar coordinates representation and curve tree.Journal of theoretical biology · 2012Article
- Theoretical study of GSK-3α: neural networks QSAR studies for the design of new inhibitors using 2D descriptors.Molecular diversity · 2011Article
- Disease embryo development network reveals the relationship between disease genes and embryo development genes.Journal of theoretical biology · 2011Article
- The disposition of the LZCC protein residues in wenxiang diagram provides new insights into the protein-protein interaction mechanism.Journal of theoretical biology · 2011Article
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2 authors.
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Abstract
In this article, we introduce three 3D graphical representations of DNA primary sequences, which we call RY-curve, MK-curve and SW-curve, based on three classifications of the DNA bases. The advantages of our representations are that (i) these 3D curves are strictly non-degenerate and there is no loss of information when transferring a DNA sequence to its mathematical representation and (ii) the coordinates of every node on these 3D curves have clear biological implication. Two applications of these 3D curves are presented: (a) a simple formula is derived to calculate the content of the four bases (A, G, C and T) from the coordinates of nodes on the curves; and (b) a 12-component characteristic vector is constructed to compare similarity among DNA sequences from different species based on the geometrical centers of the 3D curves. As examples, we examine similarity among the coding sequences of the first exon of beta-globin gene from eleven species and validate similarity of cDNA sequences of beta-globin gene from eight species.
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