The ViennaRNA web services.

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.

[1]  P. Stadler,et al.  Bcheck: a wrapper tool for detecting RNase P RNA genes , 2010, BMC Genomics.

[2]  Christian Höner zu Siederdissen,et al.  CMCompare webserver: comparing RNA families via covariance models , 2013, Nucleic Acids Res..

[3]  I. Hofacker,et al.  Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. , 2004, Journal of molecular biology.

[4]  Stephan H. Bernhart,et al.  Strategies for measuring evolutionary conservation of RNA secondary structures , 2008, BMC Bioinformatics.

[5]  Peter F. Stadler,et al.  Thermodynamics of RNA-RNA Binding , 2006, German Conference on Bioinformatics.

[6]  Kristin Reiche,et al.  RNAstrand: reading direction of structured RNAs in multiple sequence alignments , 2007, Algorithms for Molecular Biology.

[7]  Peter F. Stadler,et al.  ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.

[8]  Michael T. Wolfinger,et al.  Barrier Trees of Degenerate Landscapes , 2002 .

[9]  Peter F. Stadler,et al.  RNAz 2.0: Improved Noncoding RNA Detection , 2010, Pacific Symposium on Biocomputing.

[10]  P. Stadler,et al.  Secondary structure prediction for aligned RNA sequences. , 2002, Journal of molecular biology.

[11]  Ivo L. Hofacker,et al.  Vienna RNA secondary structure server , 2003, Nucleic Acids Res..

[12]  Hakim Tafer,et al.  Designing optimal siRNA based on target site accessibility. , 2010, Methods in molecular biology.

[13]  Peter F. Stadler,et al.  Partition function and base pairing probabilities of RNA heterodimers , 2006, Algorithms for Molecular Biology.

[14]  E. Rivas,et al.  The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective , 2013, RNA biology.

[15]  Rolf Backofen,et al.  Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA , 2010, Nucleic Acids Res..

[16]  Sebastian Will,et al.  RNAalifold: improved consensus structure prediction for RNA alignments , 2008, BMC Bioinformatics.

[17]  Michael T. Wolfinger,et al.  Efficient computation of RNA folding dynamics , 2004 .

[18]  Stefan Washietl,et al.  Sequence and structure analysis of noncoding RNAs. , 2010, Methods in molecular biology.

[19]  Peter F Stadler,et al.  Fast and reliable prediction of noncoding RNAs , 2005, Proc. Natl. Acad. Sci. USA.

[20]  Ivo L. Hofacker,et al.  AREsite: a database for the comprehensive investigation of AU-rich elements , 2010, Nucleic Acids Res..

[21]  Ronny Lorenz,et al.  The Vienna RNA Websuite , 2008, Nucleic Acids Res..

[22]  D. Turner,et al.  Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Peter F. Stadler,et al.  RNApredator: fast accessibility-based prediction of sRNA targets , 2011, Nucleic Acids Res..

[24]  Stefan L Ameres,et al.  The impact of target site accessibility on the design of effective siRNAs , 2008, Nature Biotechnology.

[25]  Ivo L. Hofacker,et al.  The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures , 2007, Nucleic Acids Res..

[26]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[27]  Ronny Lorenz,et al.  Predicting RNA structure: advances and limitations. , 2014, Methods in molecular biology.

[28]  P. Schuster,et al.  Complete suboptimal folding of RNA and the stability of secondary structures. , 1999, Biopolymers.