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On 3D graphical representation of RNA secondary structures and their applications

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In this article, we proposed a 3D representation of RNA secondary structures. Based on this representation, we outline an approach by constructing a 3-component vector whose components are the normalized leading eigenvalues of the L/L matrices associated with RNA secondary structure. The examination of similarities/dissimilarities among the secondary structure at the 3’-terminus of different viruses illustrates the utility of the approach.

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References

  1. Randic M., Vracko M., Nandy A., Basak S.C. (2000) J. Chem. Inf. Comput. Sci. 40: 1235–1244

    Article  CAS  Google Scholar 

  2. Randic M., Vracko M., Lers N., plavsic D. (2003) Chem. Phys. Lett. 371: 202–207

    Article  CAS  Google Scholar 

  3. Nandy A., Nandy P. (2003) Chem. Phys. Lett. 368: 102–107

    Article  CAS  Google Scholar 

  4. Liao B., Ding K. (2005) J. Comput. Chem. 26: 1519–1523

    Article  CAS  Google Scholar 

  5. Liao B. (2005) Chem. Phys. Lett. 401: 196–199

    Article  CAS  Google Scholar 

  6. Liao B., Shan X., Zhu W., Li R. (2006) Chem. Phys. Lett. 422: 282–288

    Article  CAS  Google Scholar 

  7. Liao B., Tan M., Ding K. (2005) Chem. Phys. Lett. 414: 296–300

    Article  CAS  Google Scholar 

  8. Zhu W., Liao B., Ding K. (2005) J. Mol. Struct. THEOCHEM 757: 193–198

    Article  CAS  Google Scholar 

  9. Liao B., Luo J., Li R., Zhu W. (2006) Int. J. Quantum. Chem. 106(8): 1749–1755

    Article  CAS  Google Scholar 

  10. J. Luo, B. Liao, R. Li and W. Zhu, J. Math. Chem (online first).

  11. Yao Y., Nan X., Wang T., (2005) J. Comput. Chem. 26: 1339–1346

    Article  CAS  Google Scholar 

  12. Chantal B.E.M., Reusken J.F. (1996) Bol, Nucl. Acids. Res. 14: 2660–2665

    Google Scholar 

  13. Koper-Zwarthoff E.C., Brederode F.Th., Walstra P., Bol J.F. (1979) Nucl. Acids. Res. 7: 1887–1900

    Article  CAS  Google Scholar 

  14. Scott S.W., Ge X. (1995) J. Gen. Virol. 76: 957–963

    CAS  Google Scholar 

  15. Koper-Zwarthoff E.C., Brederode F.Th., Walstra P., Bol J.F. (1980) Nucl. Acids. Res. 8: 3307–3318

    Article  CAS  Google Scholar 

  16. Cornelissen B.J., Janssen H., Zuidema D., Bol J.F. (1984) Nucl. Acids. Res. 12: 2427-2437

    Article  CAS  Google Scholar 

  17. Alrefai R.H., Shicl P., Domier L.L., D’Arcy C.J., Berger P.H., Korban S.S. (1994) J. Gen. Virol. 75: 2847–2850

    CAS  Google Scholar 

  18. Scott S.W., Ge X., (1995) J. Gen. Virol. 76: 1801–1806

    Article  CAS  Google Scholar 

  19. Bachman E.J., Scott S.W., Xin G., Bowman Vance V. (1994). Virology 201: 127–131

    Article  CAS  Google Scholar 

  20. Houser-Scott F., Baer M.L., Liem K.F., Cai J.M., Gehrke L. (1994) J. Virol 68: 2194–2205

    CAS  Google Scholar 

  21. EMBL/GenBank/DDBJ databases. Accession no.X86352.

  22. Randic M., Vracko M., Lers N. (2003) Plavsic D. Chem. Phys. Lett. 368: 1–6

    Article  CAS  Google Scholar 

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Correspondence to Liwei Liu.

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Liu, L., Wang, T. On 3D graphical representation of RNA secondary structures and their applications. J Math Chem 42, 595–602 (2007). https://doi.org/10.1007/s10910-006-9135-4

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  • DOI: https://doi.org/10.1007/s10910-006-9135-4

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