Graphic mapping of protein-coding DNA sequence in four-dimensional space and its application

Journal of Computational and Theoretical Nanoscience

Volumn 11, Issue 5, 2014, Pages 1244-1251

  Qi, Xiao Qin ^a   Li, Xiao Hong ^a   Qi, Zhao Hui ^a  

^a SHIJIAZHUANG TIEDAO UNIVERSITY   (China)

Author keywords

Alignment free genome comparison; Phylogenetic tree; Protein coding DNA sequence; Sequence analysis

Indexed keywords

ALIGNMENT-FREE GENOME COMPARISONS; FOUR-DIMENSIONAL SPACE; ITS APPLICATIONS; MITOCHONDRIAL GENOMES; PHYLOGENETIC TREES; PROTEIN-CODING; SEQUENCE ANALYSIS; STATISTICAL CHARACTERISTICS;

ALIGNMENT; AMINO ACIDS; BIOINFORMATICS; GENES; GRAPHIC METHODS; PROTEINS;

DNA SEQUENCES;

EID: 84896797052     PISSN: 15461955     EISSN: 15461963     Source Type: Journal    
DOI: 10.1166/jctn.2014.3489     Document Type: Article

References (55)

1. K. C. Chou, Curr. Proteomics 6, 262 (2009).
2. K. C. Chou, Eur. J. Biochem. 113, 195 (1980).
3. G. P. Zhou and M. H. Deng, Biochem. J. 222, 169 (1984).
4. K. C. Chou, Biophysical Chemistry 35, 1 (1990).
5. J. Andraos, Can. J. Chem. 86, 342 (2008).
6. K. C. Chou, Curr. Drug Metab. 11, 369 (2010).
7. H. B. Shen, J. N. Song, and K. C. Chou, J. Biomed. Sci. Eng. 2, 136 (2009).
8. C. T. Zhang and K. C. Chou, J. Protein Chem. 12, 329 (1993).
9. C. T. Zhang and K. C. Chou, J. Mol. Biol. 238, 1 (1994).
10. X. Xiao, S. H. Shao, Y. S. Ding, Z. D. Huang, and K. C. Chou, Amino Acids 30, 49 (2006).
11. X. Xiao, S. H. Shao, and K. C. Chou, Biochem. Bioph. Res. Co. 342, 605 (2006).
12. X. Xiao, S. Shao, Y. Ding, Z. Huang, X. Chen, and K. C. Chou, J. Theor. Biol. 235, 555 (2005).
13. K. Sorimachi and T. Okayasu, Biol. Lett. 271, S127 (2004).
14. G. P. Zhou, J. Theor. Biol. 284, 142 (2011).
15. N. Kurochkina and T. Choekyi, J. Theor. Biol. 283, 92 (2011).
16. G. P. Zhou, Proteins Peptide Lett. 18, 966 (2011).
17. K. C. Chou, W. Z. Lin, and X. Xiao, Nat. Sci. 3, 862 (2011).
18. E. Hamori and J. Ruskin, J. Biol. Chem. 258, 1318 (1983).
19. E. Hamori, Biotechniques 7, 710 (1989).
20. H. J. Jeffrey, Nucleic Acids Res. 18, 2163 (1990).
21. M. A. Gates, J. Theor. Biol. 119, 319 (1986).
22. A. Nandy, Curr. Sci. 66, 309 (1994).
23. P. M. Leong and S. Mogenthaler, Comput. Appl. Biosci. 12, 503 (1995).
24. M. Randić, M. Vračko, A. Nandy, and S. C. Basak, J. Chem. Inf. Comp. Sci. 40, 1235 (2000).
25. M. Randić, M. Vračko, L. Nella, and P. Dejan, Chem. Phys. Lett. 368, 1 (2003).
26. M. Randić, Chem. Phys. Lett. 456, 84 (2008).
27. M. Randić, J. Zupan, and T. Pisanski, J. Math. Chem. 43, 674 (2008).
28. D. Bielińska-Wa{ogonek}ż, J. Math. Chem. 47, 41 (2010).
29. D. Bielińska-Wa{ogonek}ż and S. Subramaniam, J. Theor. Biol. 266, 667 (2010).
30. M. Novic and M. Randić, Sar. Qsar. Environ. Res. 19, 317 (2008).
31. G. Jaklic, T. Pisanski, and M. Randić, J. Comput. Biol. 13, 1558 (2006).
32. Y. H. Yao, X. Y. Nan, and T. M. Wang, J. Mol. Struct. THEOCHEM 764, 101 (2006).
33. Y. H. Yao, Q. Dai, X. Y. Nan, P. A. He, Z. M. Nie, S. P. Zhou, and Y. Z. Zhang J. Comput. Chem. 2, 1632 (2008).
34. Y. H. Yao, Q. Dai, L. Li, X. Y. Nan, P. A. He, and Y. Z. Zhang, J. Comput. Chem. 31, 1045 (2010).
35. Z. H. Qi, L. Li, and X. Q. Qi, J. Comput. Chem. 32, 3233 (2011).
36. Z. H. Qi and X. Q. Qi, Chem. Phys. Lett. 440, 139 (2007).
37. Z. H. Qi and X. Q. Qi, Comput. Biol. Med. 39, 388 (2009).
38. Z. H. Qi, J. Feng, X. Q. Qi, and L. Li, Comput. Biol. Med. 42, 556 (2012).
39. Z. J. Zhang, X. X. Zeng, and T. Song, J. Comput. Theor. Nanos. 10, 189 (2013).
40. L. Huang, H. L. Tan, and B. Liao, J. Comput. Theor. Nanos. 10, 257 (2013).
41. M. Randić, J. Zupan, A. T. Balaban, D. Vikić-Topić and D. Plavs¡ić, Chem. Rev. 111, 790 (2011).
42. D. Bielińska-Wa{ogonek}ż, J. Math. Chem. 49, 2345 (2011).
43. L. Wang and T. Jiang, J. Comput. Biol. 13, 1323 (1994).
44. J. Qi, B. Wang, and B. Hao, J. Mol. Evol. 58, 1 (2004).
45. M. Deng, C. Yu, Q. Liang, R. L. He, and S. S.-T. Yau, PLoS ONE 6, e17293 (2011).
46. P. K. Bose, N. Paitya, S. Bhattacharya, D. De, S. Saha, K. M. Chatterjee, S. Pahari, and K. P. Ghatak, Quantum Matter 1, 89 (2012).
47. B. Tüzün and C. Erkoç, Quantum Matter 1, 136 (2012).
48. T. Ono, Y. Fujimoto, and S. Tsukamoto, Quantum Matter 1, 4 (2012).
49. A. Herman, Rev. Theor. Sci. 1, 3 (2013).
50. E. L. Pankratov and E. A. Bulaeva, Rev. Theor. Sci. 1, 58 (2013).
51. Q. Y. Zhao, Rev. Theor. Sci. 1, 83 (2013).
52. A. Khrennikov, Rev. Theor. Sci. 1, 34 (2013).
53. W. M. Brown, E. M. Prager, A. Wang, and A. C. Wilson, J. Mol. Evol. 18, 225 (1982).
54. C. Kimchi-Sarfaty, J. M. Oh, I. W. Kim, Z. E. Sauna, A. M. Calcagno, S. V. Ambudkar, and M. M. Gottesman, Science 315, 525 (2007).
55. K. C. Chou and H. B. Shen, Nat. Sci. 2, 63 (2009).