ArticleJournal of molecular modeling2014
3D-dynamic representation of DNA sequences.
Article in Journal of molecular modeling, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Visualization Methods for DNA Sequences: A Review and Prospects.Biomolecules · 2024Review
- Classification Maps: A New Mathematical Tool Supporting the Diagnosis of Age-Related Macular Degeneration.Journal of personalized medicine · 2023Article
- Non-standard bioinformatics characterization of SARS-CoV-2.Computers in biology and medicine · 2021Article
- A new graph-theoretic approach to determine the similarity of genome sequences based on nucleotide triplets.Genomics · 2020Article
- Measuring Similarity among Protein Sequences Using a New Descriptor.BioMed research international · 2019Article
- A degeneration-reducing criterion for optimal digital mapping of genetic codes.Computational and structural biotechnology journal · 2019Article
- One novel representation of DNA sequence based on the global and local position information.Scientific reports · 2018Article
- Novel Method of 3-Dimensional Graphical Representation for Proteins and Its Application.Evolutionary bioinformatics online · 2018Article
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Authors and funding
2 authors.
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Abstract
A new 3D graphical representation of DNA sequences is introduced. This representation is called 3D-dynamic representation. It is a generalization of the 2D-dynamic dynamic representation. The sequences are represented by sets of "material points" in the 3D space. The resulting 3D-dynamic graphs are treated as rigid bodies. The descriptors characterizing the graphs are analogous to the ones used in the classical dynamics. The classification diagrams derived from this representation are presented and discussed. Due to the third dimension, "the history of the graph" can be recognized graphically because the 3D-dynamic graph does not overlap with itself. Specific parts of the graphs correspond to specific parts of the sequence. This feature is essential for graphical comparisons of the sequences. Numerically, both 2D and 3D approaches are of high quality. In particular, a difference in a single base between two sequences can be identified and correctly described (one can identify which base) by both 2D and 3D methods.
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