Comparative Analysis of RNA Genes

The caRNAc Software
  • Hélène Touzet
Part of the Methods in Molecular Biology™ book series (MIMB, volume 395)

Summary

RNA genes are ubiquitous in the cell and are involved in a number of biochemical processes. Because there is a close relationship between function and structure, software tools that predict the secondary structure of noncoding RNAs from the base sequence are very helpful. In this article, we focus our attention on the inference of conserved secondary structure for a group of homologous RNA sequences. We present the caRNAc software, which enables the analysis of families of homologous sequences without prior alignment. The method relies both on comparative analysis and thermodynamic information.

Keywords

RNA in silico folding structure prediction comparative analysis thermodynamic model. 

References

  1. 1.
    Eddy, S. R. (2001) Non-coding RNA genes and the modern RNA world. Nat. Rev. Gen. 2, 919–929.CrossRefGoogle Scholar
  2. 2.
    Eddy, S. R. (2004) How do RNA folding algorithms work. Nat. Biotechnol. 22, 1457–1458.CrossRefPubMedGoogle Scholar
  3. 3.
    Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406–3415.CrossRefPubMedGoogle Scholar
  4. 4.
    Zuker, M., Mathews, D. H., and Turner, D. H. (1999) Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide, in RNA Biochemistry and Biotechnology, (Barciszewski, J. and Clark, B.F.C., eds.), Kluwer Academic Publishers, Dordrecht/Norwell, MA.Google Scholar
  5. 5.
    Hofacker, I. L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res. 31, 3429–3431.CrossRefPubMedGoogle Scholar
  6. 6.
    Brown, J. W. and Ellis, J. C. (2005) Comparative analysis of RNA secondary structure: the 6S RNA, in Handbook of RNA Biochemistry, (Bindereif, A., Hartmann, R., Schön, A., and Westhof, E., eds.), Wiley-VCH, Weinheim, Germany.Google Scholar
  7. 7.
    Gardner, P., Wilm, A., and Washietl, S. (2005) A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res. 33, 2433–2439.CrossRefPubMedGoogle Scholar
  8. 8.
    Perriquet, O., Touzet, H., and Dauchet, M. (2003) Finding the common structure shared by two homologous RNAs. Bioinformatics 19, 108–116.CrossRefPubMedGoogle Scholar
  9. 9.
    Touzet, H. and Perriquet, O. (2004) CARNAC: folding families of non coding RNAs. Nucleic Acids Res. 142, W142–W145.CrossRefGoogle Scholar
  10. 10.
    Gardner, P. and Giegerich, R. (2005) A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 5, 140.CrossRefGoogle Scholar
  11. 11.
    Bruccoleri, R. and Heinrich, G. (1988) An improved algorithm for nucleic acid secondary structure display. Comput. Appl. Biosci. 4, 167–173.PubMedGoogle Scholar
  12. 12.
    Hofacker, I. L., Fekete, M., and Stadler, P. F. (2002) Secondary structure prediction for aligned RNA sequences. J. Mol. Biol. 319, 1059–1066.CrossRefPubMedGoogle Scholar
  13. 13.
    Higgins, D., Thompson, J., Gibson, T., Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressivemultiple sequence alignment through sequence weighting,position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680.CrossRefPubMedGoogle Scholar
  14. 14.
    Xayaphoummine, A., Bucher, T., and Isambert, H. (2005) Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots, Nucleic Acid Res. 33, 605–610.CrossRefGoogle Scholar
  15. 15.
    Ji, Y., Xu, X., and Stormo, G. D. (2004) A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. Bioinformatics 20, 1591–1602.Google Scholar

Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Hélène Touzet
    • 1
  1. 1.LIFL-batiment M3, Cité Scientifique, Université desSciences et Technologies de LilleFrance

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