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Journal of Information Science and Engineering, Vol. 23 No. 6, pp. 1723-1736


Global Visualization and Comparison of DNA Sequences by Use of Three-Dimensional Trajectories

Neng-Wen Lo, Hsuan T. Chang+, S. W. Xiao+, C. H. Li+ and Chung J. Kuo++
Department of Animal Science and Biotechnology 
Tunghai University 
Taichung, 407 Taiwan 
+Department of Electrical Engineering 
National Yunlin University of Science and Technology 
Yunlin, 640 Taiwan 
++Magnetics & Microwave Business Unit 
Components Business Group, Delta Electronics, Inc. 
Taoyuan, 333 Taiwan

    In this study, the three-dimensional (3-D) trajectory (TDT) method for deoxyribonucleic acid (DNA) sequence visualization and comparison is proposed. The global view of a DNA sequence in any sizes can be easily graphically represented by a TDT and examined for sequence characteristics. Studies of the TDTs of known DNA sequences and computer-generated sequences reveal significant pattern disparity. This pattern disparity may be helpful in monitoring the deliberate deposition of false sequences in public domains. The TDTs of the sequences from homologous and non-homologous genes are also manifested. In addition to the high efficiency in space utilization for graphical representation, the visual discrimination and quantitatively representation of the similarities among DNA sequences can also be achieved by the proposed method. Our visualization method is worthy of further exploitation as part of an annotation pipeline to identify highly homologous sequences in databases.

Keywords: bioinformatics, graphical representation, sequence visualization, three-dimensional trajectory, DNA sequence

  Retrieve PDF document (JISE_200706_05.pdf)