Similarity analysis of DNA sequences based on a compact representation

Proceedings 2010 IEEE 5th International Conference on Bio-Inspired Computing: Theories and Applications, BIC-TA 2010

Volumn , Issue , 2010, Pages 1143-1146

  Zhang, Zhujin ^a,b   Wang, Shuo ^a   Zhang, Xingyi ^c   Zhang, Zheng ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b UNIVERSITY OF SOUTH AUSTRALIA   (Australia)

^c ANHUI UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COMPACT REPRESENTATION; DESCRIPTORS; FAST ALGORITHMS; GLOBIN GENE; GRAPHICAL REPRESENTATIONS; SIMILARITY ANALYSIS; TIME COMPLEXITY;

COMPUTATION THEORY; COVARIANCE MATRIX; DNA; GRAPHIC METHODS;

DNA SEQUENCES;

EID: 78650607000     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BICTA.2010.5645092     Document Type: Conference Paper

References (25)

1. E. Hamori and J. Ruskin, "H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences, " J. Biol Chem., vol. 258, no. 2, pp. 1318-27, Jan 1983.
2. E. Hamori, "Novel DNA sequence representations, " Nature, vol. 314, no. 6012, pp. 585-586, Apr 1985.
3. M. A. Gates, "Simpler DNA sequence representations, " Nature, vol. 316, no. 6025, p. 219, Jul 1985.
4. A. Nandy, "A new graphical representation and analysis of DNA sequence structure: I. Methodology and application to globin genes, " Curr. Sci., vol. 66, pp. 309-314, Jul 1994.
5. X. Guo, M. Randic, and S. Basak, "A novel 2-D graphical representation of DNA sequences of low degeneracy, " Chem. Phys. Lett., vol. 350, no. 1-2, pp. 106-112, Dec 2001.
6. Y. Wu, A. Liew, H. Yan, and M. Yang, "DB-Curve: a novel 2D method of DNA sequence visualization and representation, " Chem. Phys. Lett., vol. 367, no. 1-2, pp. 170-176, Jan 2003.
7. R. Zhang and C. Zhang, "Z curves, an intutive tool for visualizing and analyzing the DNA sequences, " J. Biomol. Struct. Dyn., vol. 11, pp. 767-782, Feb 1994.
8. C. Zhang, R. Zhang, and H. Ou, "The Z curve database: a graphic representation of genome sequences, " Bioinformatics, vol. 19, no. 5, pp. 593-599, Mar 2003.
9. Z.-H. Qi and T.-R. Fan, "PN-curve: A 3D graphical representation of DNA sequences and their numerical characterization, " Chem. Phys. Lett., vol. 442, no. 4-6, pp. 434-440, Jul 2007.
10. X.-Q. Qi, J. Wen, and Z.-H. Qi, "New 3D graphical representation of DNA sequence based on dual nucleotides, " J. Theor. Biol., vol. 249, no. 4, pp. 681-690, Dec 2007.
11. J.-F. Yu, X. Sun, and J.-H. Wang, "TN curve: A novel 3D graphical representation of DNA sequence based on trinucleotides and its applications, " J. Theor. Biol., vol. 261, no. 3, pp. 459-468, DEC 7 2009.
12. J.-F. Yu, J.-H. Wang, and X. Sun, "Analysis of Similarities/ Dissimilarities of DNA Sequences Based on a Novel Graphical Representation, " MATCH Commun. Math. Comput. Chem., vol. 63, no. 2, pp. 493-512, 2010.
13. M. Randić, M. Vračko, N. Lerš, and D. Plavšić, "Novel 2-D graphical representation of DNA sequences and their numerical characterization, " Chem. Phys. Lett., vol. 368, no. 1-2, pp. 1-6, Jan 2003.
14. B. Liao, "A 2D graphical representation of DNA sequence, " Chem. Phys. Lett, vol. 401, no. 1-3, pp. 196-199, JAN 1 2005.
15. G. Huang, B. Liao, Y. Li, and Z. Liu, "H-L curve: A novel 2D graphical representation for DNA sequences, " Chem. Phys. Lett., vol. 462, no. 1-3, pp. 129-132, Sep 2008.
16. Z. Zhang, "DV-Curve: a novel intuitive tool for visualizing and analyzing DNA sequences, " Bioinformatics, vol. 25, no. 9, pp. 1112-1117, May 2009.
17. H. Jeffrey, "Chaos game representation of gene structure, " Nucleic Acids Res., vol. 18, no. 8, pp. 2163-2170, Jul 1990.
18. M. Randić, M. Vračko, J. Zupan, and M. Novič, "Compact 2-D graphical representation of DNA, " Chem. Phys. Lett., vol. 373, no. 5-6, pp. 558-562, May 28 2003.
19. M. Beeler and Paterson, Worm: Artificial Intelligence Memo. Massachusetts Institute of Technology, May 1973.
20. M. Gardner, Knotted Doughnuts and Other Mathematical Entertainments. New York: W.H. Freeman and Co., 1986.
21. M. Randić, M. Vračko, N. Lerš, and D. Plavšić, "Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation, " Chem. Phys. Lett., vol. 371, no. 1-2, pp. 202-207, Mar 2003.
22. I. Pesek and J. Zerovnik, "A numerical characterization of modified Hamori curve representation of DNA sequences, " MATCH Commun. Math. Comput. Chem., vol. 60, no. 2, pp. 301-312, 2008.
23. B. Liao, C. Zeng, F. Li, and Y. Tang, "Analysis of similarity/dissimilarity of DNA sequences based on dual nucleotides, " MATCH Commun. Math. Comput. Chem., 2008.
24. Z. Liu, B. Liao, and W. Zhu, "A New Method to Analyze the Similarity Based on Dual Nucleotides of the DNA Sequence, " MATCH Commun. Math. Comput. Chem., vol. 61, no. 2, pp. 541-552, 2009.
25. B. Liao, M. Tan, and K. Ding, "Application of 2-D graphical representation of DNA sequence, " Chem. Phys. Lett., vol. 414, no. 4-6, pp. 296-300, Oct 2005.