Journal of Mathematical Biology

, Volume 56, Issue 1–2, pp 129–144 | Cite as

Variations on RNA folding and alignment: lessons from Benasque

  • Athanasius F. Bompfünewerer
  • Rolf Backofen
  • Stephan H. Bernhart
  • Jana Hertel
  • Ivo L. Hofacker
  • Peter F. Stadler
  • Sebastian Will
Article

Abstract

Dynamic programming algorithms solve many standard problems of RNA bioinformatics in polynomial time. In this contribution we discuss a series of variations on these standard methods that implement refined biophysical models, such as a restriction of RNA folding to canonical structures, and an extension of structural alignments to an explicit scoring of stacking propensities. Furthermore, we demonstrate that a local structural alignment can be employed for ncRNA gene finding. In this context we discuss scanning variants for folding and alignment algorithms.

Keywords

RNA folding Secondary structure alignment Dynamic programming 

Mathematics Subject Classification (2000)

90C27 90C90 92C40 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Backofen R. and Will S. (2004). Local sequence–structure motifs in RNA. J. Bioinform. Comput. Biol. 2: 681–698 CrossRefGoogle Scholar
  2. 2.
    Bernhart S., Hofacker I.L. and Stadler P.F. (2006). Local RNA base pairing probabilities in large sequences. Bioinformatics 22: 614–615 CrossRefGoogle Scholar
  3. 3.
    Deng W., Zhu X., Skogerbø G., Zhao Y., Fu Z., Wang Y., He Housheng Cai L., Sun H., Liu C., Li B.L., Bai B., Wang J., Cui Y., Jai D., Wang Y., Du D. and Chen R. (2006). Organisation of the Caenorhabditis elegans small noncoding transiptome: genomic features, biogenesis and expression. Genome Res. 16: 30–36 Google Scholar
  4. 4.
    Ding, Y., Chan, C.Y., Lawrence, C.E.: Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 32(Web Server issue), W135–W141 (2004)Google Scholar
  5. 5.
    Doench J.G. and Sharp P.A. (2004). of mioRNA target selection in translational repression. Genes Dev. 18: 504–511 CrossRefGoogle Scholar
  6. 6.
    Dulucq S. and Tichit L. (2003). Secondary structure comparison: exact analysis of the Zhang-Shasha tree-edit algorithm. Theor. Comput. Sci. 306: 471–484 MATHCrossRefMathSciNetGoogle Scholar
  7. 7.
    Hofacker I.L. (2003). Vienna RNA secondary structure server. Nucleic Acids Res. 31: 3429–3431 CrossRefGoogle Scholar
  8. 8.
    Hofacker I.L., Bernhart S.H.F. and Stadler P.F. (2004). Alignment of RNA base pairing probability matrices. Bioinformatics 20: 2222–2227 CrossRefGoogle Scholar
  9. 9.
    Hofacker I.L., Fontana W., Stadler P.F., Bonhoeffer S., Tacker M. and Schuster P. (1994). Fast folding and comparison of RNA secondary structures. Monatsh. Chem. 125(2): 167–188 CrossRefGoogle Scholar
  10. 10.
    Hofacker I.L., Priwitzer B. and Stadler P.F. (2004). Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics 20: 191–198 CrossRefGoogle Scholar
  11. 11.
    Jiang T., Lin G., Ma B. and Zhang K. (2002). A general edit distance between RNA structures. J. Comput. Biol. 9: 371–88 CrossRefGoogle Scholar
  12. 12.
    Klein R.J. and Eddy S.R. (2003). RSEARCH: finding homologs of single structured RNA sequences. BMC Bioinform 4(1): 44 CrossRefGoogle Scholar
  13. 13.
    Leydold, J., Stadler, P.F.: Minimal cycle basis of outerplanar graphs. Elec. J. Comb. 5, 209–222 [R16: 14 p.] (1998)Google Scholar
  14. 14.
    Lin, G.H., Ma, B., Zhang, K.: Edit distance between two RNA structures. In: Proceedings of the 5th Annual International Conference on Computational Biology RECOMB01, pp. 211–220. ACM Press (2001)Google Scholar
  15. 15.
    Lyngsø R.B., Zuker M. and Pedersen C.N. (1999). Fast evaluation of internal loops in RNA secondary structure prediction. Bioinformatics 15: 440–445 CrossRefGoogle Scholar
  16. 16.
    Mathews D., Sabina J., Zuker M. and Turner H. (1999). Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. J. Mol. Biol. 288: 911–940 CrossRefGoogle Scholar
  17. 17.
    Mathews D.H., Disney M.D., Childs J.L., Schroeder S.J., Zuker M. and Turner D.H. (2004). Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA 101: 7287–7292 CrossRefGoogle Scholar
  18. 18.
    McCaskill J.S. (1990). The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29: 1105–1119 CrossRefGoogle Scholar
  19. 19.
    Mückstein U., Tafer H., Hackermüller J., Bernhart S., Stadler P.F. and Hofacker I.L. (2006). Thermodynamics of RNA-RNA binding. Bioinformatics 22: 1177–1182 CrossRefGoogle Scholar
  20. 20.
    Sankoff D. (1985). Simultaneous solution of the RNA folding, alignment and proto-sequence problems. SIAM J. Appl. Math. 45: 810–825 MATHCrossRefMathSciNetGoogle Scholar
  21. 21.
    Shao, Y., Wu, Y., Chan, C.Y., Mcdonough, K., Ding, Y.: Rational design and rapid seening of antisense oligonucleotides for prokaryotic gene modulation. Nucleic Acids Res. 34, 5660–5669 (2006)Google Scholar
  22. 22.
    Stricklin, S.L., Griffiths-Jones, S., Eddy, S.R.: C. elegans noncoding RNA genes. WormBook doi:10.1895/wormbook.1.7.1. http://www.wormbook.org/chapters/www_noncodingRNA/noncoding RNA.html (2005)Google Scholar
  23. 23.
    Tinoco I., Uhlenbeck O.C. and Levine M.D. (1971). Estimation of secondary structure in ribonucleic acids. Nature 230: 362–367 CrossRefGoogle Scholar
  24. 24.
    Will, S., Reiche, K., Hofacker, I.L., Stadler, P.F., Backofen, R.: Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comp. Biol. 3, e65 (2007)Google Scholar
  25. 25.
    Zemann A., op de Bekke A., Kiefmann M., Brosius J. and Schmitz J. (2006). Evolution of small nucleolar RNAs in nematodes. Nucleic Acids Res. 34: 2676–2685 CrossRefGoogle Scholar
  26. 26.
    Zuker M. and Sankoff D. (1984). RNA secondary structures and their prediction. Bull. Math. Biol. 46: 591–621 MATHGoogle Scholar
  27. 27.
    Zuker M. and Stiegler P. (1981). Optimal computer folding of larger RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9: 133–148 CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Athanasius F. Bompfünewerer
    • 1
    • 2
  • Rolf Backofen
    • 3
  • Stephan H. Bernhart
    • 2
  • Jana Hertel
    • 4
  • Ivo L. Hofacker
    • 2
  • Peter F. Stadler
    • 2
    • 4
    • 5
  • Sebastian Will
    • 3
  1. 1.Zentralfriedhof WienWienAustria
  2. 2.Department of Theoretical ChemistryUniversity of ViennaWienAustria
  3. 3.Bioinformatics Group, Department of Computer ScienceUniversity of FreiburgFreiburgGermany
  4. 4.Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for BioinformaticsUniversity of LeipzigLeipzigGermany
  5. 5.Santa Fe InstituteSanta FeUSA

Personalised recommendations