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Journal of Information Science and Engineering, Vol. 23 No. 6, pp. 1723-1736 (November 2007)

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

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Received September 12, 2005; revised November 18, 2005 & March 28, 2006; accepted April 25, 2006.
Communicated by Chin-Teng Lin.
*This paper was partially supported by the National Science Council of Taiwan, R.O.C., under contracts No. NSC 91-2215-E-224-007 to Dr. H. T. Chang and NSC 91-2311-B-029-003 to Dr. N. W. Lo. Part of this paper was presented at the 2003 Asia Pacific Bioinformatics Conference (APBC2003).