DB-Curve: a novel 2D method of DNA sequence visualization and representation |
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| Institution: | 1. Department of Computer Engineering and Information Technology, 83 Tat Chee Avenue, City University of Hong Kong, Kowloon, Hong Kong;2. Department of Biology and Chemistry, 83 Tat Chee Avenue, City University of Hong Kong, Kowloon, Hong Kong;3. School of Electrical and Information Engineering, University of Sydney, NSW 2006, Australia;1. Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran;2. Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran;1. Frontier Science Center of Synthetic Biology (MOE), Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300072, China;2. SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China;3. Department of Physics, Tianjin University, Tianjin, 300072, China;4. State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China;1. Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Hunan 411105, PR China;2. School of Mathematics and Computer Science, Gannan Normal University, Jiangxi 341000, PR China;3. School of Mathematical Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia;1. Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA;2. Department of Systems Biology, Columbia University, New York, NY 10032, USA;3. Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA;4. Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA;5. Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA;6. Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA;7. Department of Biology, Technion – Israel Institute of Technology, Haifa 32000, Israel;8. Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA;9. Department of Biological Sciences, Columbia University, New York, NY 10032, USA;1. School of Economics and Management, Jiangsu University of Science and Technology, Zhenjiang, 212003, China;2. School of Business, Central South University, Changsha, 410083, China;3. College of Systems Engineering, National University of Defense Technology, Changsha, 410073, China;4. Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan |
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| Abstract: | The large number of bases in a DNA sequence and the cryptic nature of the 4-alphabet representation make graphical visualization of DNA sequences useful for biologists. However, existing 3D graphical representations are complicated, whereas existing 2D graphical representations suffer from high degeneracy, and many features in a DNA sequence cannot be visualized clearly. This Letter introduces a novel 2D method of DNA representation: the DB-Curve (Dual-Base Curve), which overcomes some of the limitations in existing 2D graphical representations. Many properties of DNA sequences can be observed and visualized easily using a combination of DB-Curves. The new representation can avoid degeneracy completely compared to existing 2D graphical representations of DNA sequences. Unlike 3D graphical representations, no 2D projection is required for the DB-Curve, and this allows for easier analysis of DNA sequences. The DB-Curve provides a useful graphical tool for the visualization and study of DNA sequences. |
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