RNA Secondary Structure Analysis Using the Vienna RNA Package

Ivo L. Hofacker1

1 University of Vienna‐Institute of Theoretical Chemistry, Vienna, Austria
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 12.2
DOI:  10.1002/0471250953.bi1202s26
Online Posting Date:  June, 2009
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This unit documents how to use the Vienna RNA package for RNA secondary structure analysis. Possible tasks include structure prediction for single sequences, prediction of consensus structures, prediction of RNA‐RNA interactions, and sequence design. Curr. Protoc. Bioinform. 26:12.2.1‐12.2.16. © 2009 by John Wiley & Sons, Inc.

Keywords: structure prediction; secondary structure; RNA structure; consensus structure; sequence design; RNA interactions

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Table of Contents

  • Introduction
  • Basic Protocol 1: Using the RNAfold Program to Predict RNA Secondary Structure
  • Basic Protocol 2: Computing Consensus Structures
  • Basic Protocol 3: Cofolding of Two RNA Molecules
  • Alternate Protocol 1: Predicting RNA‐RNA Interactions Using RNAduplex and RNAup
  • Basic Protocol 4: Inverse Folding
  • Alternate Protocol 2: Using the Vienna RNA Websuite
  • Support Protocol 1: Installing the Vienna RNA Package
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
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Literature Cited

   Bernhart, S.H., Tafer, H., Mückstein, U., Flamm, Ch., Stadler, P.F., and Hofacker, I.L. 2006. Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol. Biol. 1:3.
   Flamm, C., Fontana, W., Hofacker, I.L., and Schuster, P. 2000. RNA folding at elementary step resolution. RNA 6:325‐338.
   Flamm, C., Hofacker, I.L., Stadler, P.F., and Wolfinger, M.T. 2002. Barrier trees of degenerate landscapes. Z. Phys. Chem. 216:155‐173.
   Gruber, A.R., Lorenz, R., Bernhart, S.H., Neuböck, R., and Hofacker, I.L. 2008. The Vienna RNA websuite. Nucl. Acids Res. Epub, April 19, 2008.
   Hofacker, I.L. and Stadler, P.F. 1999. Automatic detection of conserved base pairing patterns in RNA virus genomes. Comput. Chem. 23:401‐414.
   Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoffer, S., Tacker, M., and Schuster, P. 1994. Fast folding and comparison of RNA secondary structures (the Vienna RNA Package). Monath. Chem. 125:167‐188.
   Hofacker, I.L., Fekete, M., Flamm, C., Huynen, M.A., Rauscher, S., Stolorz, P.E., and Stadler, P.F. 1998. Automatic detection of conserved RNA structure elements in complete RNA virus genomes. Nucl. Acids Res. 26:3825‐3836.
   Hofacker, I.L., Fekete, M., and Stadler, P.F. 2002. Secondary structure prediction for aligned RNA sequences. J. Mol. Biol. 319:1059‐1066.
   Mathews, D., Sabina, J., Zucker, M., and Turner, H. 1999. Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. J. Mol. Biol. 288:911‐940.
   McCaskill, J. 1990. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29:1105‐1119.
   Mückstein, U., Tafer, H., Hackermüller, J., Bernhart, S.H., Stadler, P.F., and Hofacker, I.L. 2006. Thermodynamics of RNA‐RNA binding. Bioinformatics 22:1177‐1182.
   Schuster, P., Fontana, W., Stadler, P.F., and Hofacker, I.L. 1994. From sequences to shapes and back: A case study in RNA secondary structures. Proc. R. Soc. London B Biol. Sci. 255:279‐284.
   Shapiro, B. and Zhang, K. 1990. Comparing multiple RNA secondary structures using tree comparisons. Comput. Appl. Biosci. 6:309‐318.
   Walter, A.E., Turner, D.H., Kim, J., Lyttle, M.H., Muller, P., Mathews, D.H., and Zuker, M. 1994. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Natl. Acad. Sci. U.S.A. 91:9218‐9222.
   Wuchty, S., Fontana, W., Hofacker, I.L., and Schuster, P. 1999. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49:145‐165.
   Zuker, M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244:48‐52.
   Zuker, M. and Stiegler, P. 1981. Optimal computer folding of larger RNA sequences using thermodynamics and auxiliary information. Nucl. Acids Res. 9:133‐148.
Key References
   Hofacker, I.L. 2003. The Vienna RNA secondary structure server. Nucl. Acids Res. 31:3429‐3431.
  Describes how to perform several of the functions discussed in this unit on the Web using the Vienna RNA server.
   Hofacker et al., 1994. See above.
  The paper describing the first release of the Vienna RNA package, including a description of the underlying algorithm.
Internet Resources
  Site at which to download the latest version of the Vienna RNA package and read online manuals.
  Web interfaces to several of the Vienna RNA programs.
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