Advertisement

Journal of Mathematical Chemistry

, Volume 43, Issue 3, pp 932–943 | Cite as

A new mapping rule for RNA secondary structures with its applications

  • Fenglan Bai
  • Dachao Li
  • Tianming Wang
Original Paper

Abstract

According to the characterization of RNA secondary structures, the RNA secondary structures are transformed into elementary sequences, namely characteristic sequences of RNA secondary structures, by representing A, U, G, C in A-U/ G-C pairs, as A′, U′, G′, C′. Based on the representation, three recurrences for mapping RNA secondary structures into 1-D graph, 2-D graph and 3-D graph are given, respectively. Furthermore, a frequency-based method for RNA secondary structures is given in terms of 1-D graph.

Keywords

RNA secondary structures Graphical representation Fourier transform 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Randic M., Vracko M. (2000) J. Chem. Inf. Comput. 40:599Google Scholar
  2. 2.
    Randic M., Vracko M., Nandy A., Basak S.C. (2000) J. Inf. Comput. 40:1235CrossRefGoogle Scholar
  3. 3.
    Randic M., Vracko M., Nella L., Dejan P. (2003) Chem. Phys. Lett. 368:1CrossRefGoogle Scholar
  4. 4.
    Randic M., Vracko M., Lers N., Plavsic D. (2003) Chem. Phy. Lett. 371:202CrossRefGoogle Scholar
  5. 5.
    Nandy A., Nandy P. (2003) Chem. Phys. Lett. 368:102CrossRefGoogle Scholar
  6. 6.
    Nandy A. (1996) Comput. Appl. Biosci. 12:55Google Scholar
  7. 7.
    Nandy A. (1994) Curr. Sci. 66:821Google Scholar
  8. 8.
    Liao B., Wang T.M. (2005) J. Comput. Chem. 11:1364Google Scholar
  9. 9.
    Liao B., Wang T.M. (2004) J. Chem. Inf. Comput. Sci. 44:1666CrossRefGoogle Scholar
  10. 10.
    Bai F.L., Wang T.M. (2006) J. Biomol. Struc. Dyn. 23:537Google Scholar
  11. 11.
    Jeffrey H.I. (1990) Nucleic Acid Res. 18:2163CrossRefGoogle Scholar
  12. 12.
    Goldman N. (1993) Nucleic Acid Res. 21:2487CrossRefGoogle Scholar
  13. 13.
    Basu S., Pan A., Dutta C., J. Das (1997) J. Mol. Graphs. Modell. 15:279CrossRefGoogle Scholar
  14. 14.
    Randic M. (2004) SAR QSAR Environ. Res. 15(3):147CrossRefGoogle Scholar
  15. 15.
    Randic M., Zupan J. (2004) SAR QSAR Environ. Res. 15(3):191CrossRefGoogle Scholar
  16. 16.
    Randic M., Zupan J., Balaban A.T. (2004) Chem. Phys. Lett. 397:247CrossRefGoogle Scholar
  17. 17.
    Randic M. (2004) Chem. Phys. Lett. 386:468CrossRefGoogle Scholar
  18. 18.
    Randic M. (2001) J. Chem. Inf. Comput. Sci. 41:1330CrossRefGoogle Scholar
  19. 19.
    Zupan J., Randic M. (2005) J. Chem. Inf. Model. 45:309CrossRefGoogle Scholar
  20. 20.
    Randic M., Butina D. (2006) J. Zupan, Chem. Phys. Lett. 419:528CrossRefGoogle Scholar
  21. 21.
    Buldyrev S.V., Goldberger A.L., Havlin S. (1995) Phys. Rev. E. 51:5084CrossRefGoogle Scholar
  22. 22.
    Anastassiou D. (2000) Bioinfor matics. 16:1073CrossRefGoogle Scholar
  23. 23.
    Bai F.L., Zhu W., Wang T.M. (2005) Chem. Phys. Lett. 408:258CrossRefGoogle Scholar
  24. 24.
    Liao B., Wang T.M. (2004) J. Biomol. Struct. Dyn. 21:827Google Scholar
  25. 25.
    Liao B., Ding K.Q., Wang T.M. (2005) J. Biomol. Struct. Dyn. 22:455Google Scholar
  26. 26.
    Zong K.D., Hu G.S. (1998) Digital Signals Disposal. Springer, Bei JingGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  1. 1.Department of MathematicsDalian Jiaotong UniversityDalianChina
  2. 2.Department of MathematicsHainan Normal UniversityHaikouChina
  3. 3.Department of Applied MathematicsDalian University of TechnologyDalianChina

Personalised recommendations