Advertisement

Journal of Mathematical Chemistry

, Volume 43, Issue 2, pp 864–873 | Cite as

Volatilities of codons and its application in similarity analysis of biological sequences

  • Yi Zhang
  • Jun Wang
Article

Volatilities of codons provide us a new way to characterize codons. In this article, we propose a new method measuring volatilities of codons base on the physics–chemical distances between amino acids and mutation frequencies between codons, then by which, we give a new graphical representation scheme for codon sequences. Finally, in order to show the effectiveness of our scheme, we analyze similarity among the coding codon sequences of exon 1 of beta-globin gene of human and those of other 10 species, find the result is consistent with those shown in the literature.

Keywords

Volatilities of codons distance mutation frequency similarity 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Staden R. (1986). Nucleic Acids Res. 14: 217–231CrossRefGoogle Scholar
  2. 2.
    Hamori E., Ruskin J. (1983). J. Biol. Chem. 258: 1318–1327Google Scholar
  3. 3.
    Hamori E. (1989). BioTechniques 7: 710–720CrossRefGoogle Scholar
  4. 4.
    Randic M., Balaban A.T. (2003). J. Chem. Inf. Comput. Sci. 43: 532–539CrossRefGoogle Scholar
  5. 5.
    Guo X.F., Randic M., Basak S.C. (2001). Chem. Phys. Lett. 350: 106–112CrossRefGoogle Scholar
  6. 6.
    Zhang R., Zhang C.T. (1994). J. Biomo. Struct. Dyn. 11: 767–782Google Scholar
  7. 7.
    Gates M.A. (1986). J. Theor. Biol. 119: 319–328CrossRefGoogle Scholar
  8. 8.
    Nandy A. (1994). Curr. Sci. 66: 309–314Google Scholar
  9. 9.
    Nandy A. (1994). Curr. Sci. 66: 821Google Scholar
  10. 10.
    Leong P.M., Mogenthaler S. (1995). Comput. Appl. Biosci. 12: 503–511Google Scholar
  11. 11.
    Guo X., Nandy A. (2003). Chem. Phys. Lett. 369: 361–366CrossRefGoogle Scholar
  12. 12.
    Wu Y., Liew A.W., Yan H., Yang M.S. (2003). Chem. Phys. Lett. 367: 170–176CrossRefGoogle Scholar
  13. 13.
    Nandy A., Nandy P. (2003). Chem. Phys. Lett. 368: 102–107CrossRefGoogle Scholar
  14. 14.
    Randic M., Vracko M., Lers N., Plavsic D. (2003). Chem. Phys. Lett. 368: 1–6CrossRefGoogle Scholar
  15. 15.
    Randic M., Vracko M., Lers N., Plavsic D. (2003). Chem. Phys. Lett. 371: 202–207CrossRefGoogle Scholar
  16. 16.
    Randic M. (2000). Chem. Phys. Lett. 317: 29–34CrossRefGoogle Scholar
  17. 17.
    Randic M., Guo X.F., Basak S.C. (2001). J. Chem. Inf. Comput. Sci. 41: 619–626CrossRefGoogle Scholar
  18. 18.
    He P., Wang J. (2002). Internet Electron. J. Mol. Des. 1: 668–674Google Scholar
  19. 19.
    He P., Wang J. (2002). J. Chem. Inf. Comput. Sci. 42: 1080–1085CrossRefGoogle Scholar
  20. 20.
    Liu Y. (2002). Internet Electron. J. Mol. Des. 1: 675–684Google Scholar
  21. 21.
    Randic M., Krilov G. (1999). Int. J. Quantum. Chem. 75: 1017–1026CrossRefGoogle Scholar
  22. 22.
    Li C., Wang J. (2003). Comb. Chem. High Throughput Screen. 6: 795–799Google Scholar
  23. 23.
    Wang J., Zhang Y. (2006). Chem. Phys. Lett. 423: 50–53CrossRefGoogle Scholar
  24. 24.
    Randic M. (2004). SAR QSAR Environ. Res. 15(3): 147–157CrossRefGoogle Scholar
  25. 25.
    Randic M., Zupan J. (2004). SAR QSAR Environ. Res. 15(3): 191–205CrossRefGoogle Scholar
  26. 26.
    Randic M., Zupan J., Balaban A.T. (2004). Chem. Phys. Lett. 397: 247–252CrossRefGoogle Scholar
  27. 27.
    Plotkin J.B., Dushoff J., Fraser H.B. (2004). Nature 428: 942–945CrossRefGoogle Scholar
  28. 28.
    Luo L., Li X. (2002). Biosystem 65: 83–97CrossRefGoogle Scholar
  29. 29.
    Grantham R.A. (1974). Sceince 185: 862–864Google Scholar
  30. 30.
    stoletzki N., Welch J., Hermisson J., Walker A.E. (2005). Mol. Biol. Evol. 22(10): 2022–2026CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  1. 1.Department of Applied MathematicsDalian University of TechnologyDalianPeople’s Republic of China
  2. 2.Department of Applied Mathematics and College of Advanced Science and TechnologyDalian University of TechnologyDalianPeople’s Republic of China

Personalised recommendations