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3D-dynamic representation of DNA sequences
- Source :
- Journal of Molecular Modeling
- Publisher :
- Springer Nature
-
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.
- Subjects :
- Models, Molecular
Generalization
Computer science
Dimension (graph theory)
DNA sequences
Bioinformatics
Zea mays
Descriptors
Catalysis
Moments of inertia
Histones
Inorganic Chemistry
Open Reading Frames
Feature (machine learning)
Computer Graphics
Animals
Humans
Physical and Theoretical Chemistry
Representation (mathematics)
Plant Proteins
Sequence
Original Paper
Organic Chemistry
Reproducibility of Results
DNA
Sequence Analysis, DNA
Base (topology)
Computer Science Applications
Computational Theory and Mathematics
Real representation
Bond graph
Algorithm
Algorithms
Subjects
Details
- Language :
- English
- ISSN :
- 16102940
- Volume :
- 20
- Issue :
- 3
- Database :
- OpenAIRE
- Journal :
- Journal of Molecular Modeling
- Accession number :
- edsair.doi.dedup.....63c0acb585534952e0c6fea7db3e7a0e
- Full Text :
- https://doi.org/10.1007/s00894-014-2141-8