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The ViennaRNA Web Services

  • Andreas R. GruberEmail author
  • Stephan H. Bernhart
  • Ronny Lorenz
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1269)

Abstract

The ViennaRNA package is a widely used collection of programs for thermodynamic RNA secondary structure prediction. Over the years, many additional tools have been developed building on the core programs of the package to also address issues related to noncoding RNA detection, RNA folding kinetics, or efficient sequence design considering RNA-RNA hybridizations. The ViennaRNA web services provide easy and user-friendly web access to these tools. This chapter describes how to use this online platform to perform tasks such as prediction of minimum free energy structures, prediction of RNA-RNA hybrids, or noncoding RNA detection. The ViennaRNA web services can be used free of charge and can be accessed via http://rna.tbi.univie.ac.at.

Key words

RNA secondary structure prediction RNA-RNA interaction prediction Noncoding RNA detection Sequence design 

Notes

Acknowledgments

This work was supported in part by the University of Basel, the Austrian FWF project “SFB F43 RNA regulation of the transcriptome,” and the University of Leipzig.

References

  1. 1.
    Hofacker IL, Fontana W, Stadler P, Bonhoeffer S, Tacker M, Schuster P (1994) Fast folding and comparison of RNA secondary structures. Monatsh Chem 125:167–188CrossRefGoogle Scholar
  2. 2.
    Lorenz R, Bernhart SH, Höner Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL (2011) ViennaRNA Package 2.0. Algorithm Mol Biol 6:26CrossRefGoogle Scholar
  3. 3.
    Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31:3429–3431PubMedCentralPubMedCrossRefGoogle Scholar
  4. 4.
    Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL (2008) The Vienna RNA websuite. Nucleic Acids Res 36:W70–W74PubMedCentralPubMedCrossRefGoogle Scholar
  5. 5.
    Hofacker IL, Fekete M, Stadler PF (2002) Secondary structure prediction for aligned RNA sequences. J Mol Biol 319:1059–1066PubMedCrossRefGoogle Scholar
  6. 6.
    Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF (2008) RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinform 9:474CrossRefGoogle Scholar
  7. 7.
    Flamm C, Hofacker IL, Stadler PF, Wolfinger MT (2002) Barrier trees of degenerate landscapes. Z Phys Chem 216:155CrossRefGoogle Scholar
  8. 8.
    Bernhart SH, Tafer H, Mückstein U, Flamm C, Stadler PF, Hofacker IL (2006) Partition function and base pairing probabilities of RNA heterodimers. Algorithm Mol Biol 1:3CrossRefGoogle Scholar
  9. 9.
    Mückstein U, Tafer H, Hackermüller J, Bernhart SH, Stadler PF, Hofacker IL (2006) Thermodynamics of RNA-RNA binding. Bioinformatics 22:1177–1182PubMedCrossRefGoogle Scholar
  10. 10.
    Eggenhofer F, Tafer H, Stadler PF, Hofacker IL (2011) RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Res 39:W149–W154PubMedCentralPubMedCrossRefGoogle Scholar
  11. 11.
    Tafer H, Ameres SL, Obernosterer G, Gebeshuber CA, Schroeder R, Martinez J, Hofacker IL (2008) The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol 26:578–583PubMedCrossRefGoogle Scholar
  12. 12.
    Washietl S, Hofacker IL (2004) Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J Mol Biol 342:19–30PubMedCrossRefGoogle Scholar
  13. 13.
    Washietl S, Hofacker IL, Stadler PF (2005) Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A 102:2454–2459PubMedCentralPubMedCrossRefGoogle Scholar
  14. 14.
    Gruber AR, Bernhart SH, Hofacker IL, Washietl S (2008) Strategies for measuring evolutionary conservation of RNA secondary structures. BMC Bioinform 9:122CrossRefGoogle Scholar
  15. 15.
    Gruber AR, Findeiß S, Washietl S, Hofacker IL, Stadler PF (2010) RNAz 2.0: improved noncoding RNA detection. Pac Symp Biocomput 2010:69Google Scholar
  16. 16.
    Gruber AR, Neuböck R, Hofacker IL, Washietl S (2007) The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures. Nucleic Acids Res 35:W335–W338PubMedCentralPubMedCrossRefGoogle Scholar
  17. 17.
    Yusuf D, Marz M, Stadler PF, Hofacker IL (2010) Bcheck: a wrapper tool for detecting RNase P RNA genes. BMC Genomics 11:432PubMedCentralPubMedCrossRefGoogle Scholar
  18. 18.
    Rivas E (2013) The four ingredients of single-sequence RNA secondary structure prediction: a unifying perspective. RNA Biol 10:59–70CrossRefGoogle Scholar
  19. 19.
    Wuchty S, Walter F, Hofacker IL, Schuster P et al (1999) Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49:145–165PubMedCrossRefGoogle Scholar
  20. 20.
    Wolfinger MT, Svrcek-Seiler AW, Flamm C, Hofacker IL, Stadler PF (2004) Efficient computation of RNA folding dynamics. J Phys Math Gen 37:4731CrossRefGoogle Scholar
  21. 21.
    Reiche K, Stadler PF (2007) RNAstrand: reading direction of structured RNAs in multiple sequence alignments. Algorithm Mol Biol 2:6CrossRefGoogle Scholar
  22. 22.
    Washietl S (2010) Sequence and structure analysis of noncoding RNAs. Methods Mol Biol 609:285–306PubMedCrossRefGoogle Scholar
  23. 23.
    Hofacker IL, Tafer H (2010) Designing optimal siRNA based on target site accessibility. Methods Mol Biol 623:137–154PubMedCrossRefGoogle Scholar
  24. 24.
    Eggenhofer F, Hofacker IL, Höner Zu Siederdissen C (2013) CMCompare webserver: comparing RNA families via covariance models. Nucleic Acids Res 41:W499–W503PubMedCentralPubMedCrossRefGoogle Scholar
  25. 25.
    Gruber AR, Fallmann J, Kratochvill F, Kovarik P, Hofacker IL (2011) AREsite: a database for the comprehensive investigation of AU-rich elements. Nucleic Acids Res 39:D66–D69PubMedCentralPubMedCrossRefGoogle Scholar
  26. 26.
    Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A 101:7287–7292PubMedCentralPubMedCrossRefGoogle Scholar
  27. 27.
    Hofacker I, Lorenz R (2014) Predicting RNA structure: advances and limitations. Methods Mol Biol 1086:1PubMedCrossRefGoogle Scholar
  28. 28.
    Smith C, Heyne S, Richter AS, Will S, Backofen R (2010) Freiburg RNA tools: a web server integrating INTARNA, EXPARNA and LOCARNA. Nucleic Acids Res 38:W373–W377PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Andreas R. Gruber
    • 1
    • 2
    Email author
  • Stephan H. Bernhart
    • 3
  • Ronny Lorenz
    • 4
  1. 1.BiozentrumUniversity of BaselBaselSwitzerland
  2. 2.Swiss Institute of BioinformaticsBaselSwitzerland
  3. 3.Department of BioinformaticsUniversity of LeipzigLeipzigGermany
  4. 4.Institute for Theoretical ChemistryUniversity of ViennaViennaAustria

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