ViennaRNA Package

ViennaRNA Package
Original author(s)	Hofacker et al.,
Developer(s)	Institut für theoretische Chemie, Währingerstr
Stable release	v2.4.17 / 25 November 2020;3 years ago
Written in	C, Perl
Operating system	Linux, macOS, Windows
Size	13.4 MB (Source)
Type	Bioinformatics
Website	www.tbi.univie.ac.at/RNA/

Last updated November 29, 2023

The ViennaRNA Package is a set of standalone programs and libraries used for prediction and analysis of RNA secondary structures. ^[1] The source code for the package is distributed freely and compiled binaries are available for Linux, macOS and Windows platforms. The original paper has been cited over 2000 times.

Background

The three dimensional structure of biological macromolecules like proteins and nucleic acids play critical role in determining their functional role.^[2] This process of decoding function from the sequence is an experimentally and computationally challenging question addressed widely.^[3]^[4] RNA structures form complex secondary and tertiary structures compared to DNA which form duplexes with full complementarity between two strands. This is partially because the extra oxygen in RNA increases the propensity for hydrogen bonding in the nucleic acid backbone. The base pairing and base stacking interactions of RNA play critical role in formation of ribosome, spliceosome, or tRNA.

Secondary structure prediction is commonly done using approaches like dynamic programming, energy minimisation (for most stable structure) and generating suboptimal structures. A large number of structure prediction tools have been implemented as well.

Development

The first version of the ViennaRNA Package was published by Hofacker et al. in 1994.^[1] The package distributed tools to compute either minimum free energy structures or partition functions of RNA molecules; both using the idea of dynamic programming. Non-thermodynamic criterion like formation of maximum matching or various versions of kinetic folding along with an inverse folding heuristic to determine structurally neutral sequences were implemented. Additionally, the package also contained a statistics suite with routines for cluster analysis, statistical geometry, and split decomposition.

The package was made available as library and a set of standalone routines.

Version 2.0

A number of major systemic changes were introduced in this version with the use of a new parametrized energy model (Turner 2004),^[5] restructuring of the RNAlib to support concurrent computations in thread-safe manner, improvements to the API, and inclusion of several new auxiliary tools. For example, tools to assess RNA-RNA interactions and restricted ensembles of structures. Furthermore, other features included additional output information such as centroid structures and maximum expected accuracy structures derived from base pairing probabilities, or z-scores for locally stable secondary structures, and support for input in FASTA format. The updates, however, are compatible with earlier versions without affecting the computational efficiency of the core algorithms.^[6]

Web server

The tools provided by the ViennaRNA Package are also available for public use through a web interface.^[7]^[8]

Tools

In addition to prediction and analysis tools, the ViennaRNA Package contains several scripts and utilities for plotting and input-output processing. A summary of the available programs is collected in the table below (an exhaustive list with examples can be found in the official documentation).^[9]

Program	Description
AnalyseDists	Analyse a distance matrix
AnalyseSeqs	Analyse a set of sequences of common length
Kinfold	Simulate kinetic folding of RNA secondary structures
RNA2Dfold	Compute MFE structure, partition function and representative sample structures of k,l neighborhoods
RNAaliduplex	Predict conserved RNA-RNA interactions between two alignments
RNAalifold	Calculate secondary structures for a set of aligned RNA sequences
RNAcofold	Calculate secondary structures of two RNAs with dimerization
RNAdistance	Calculate distances between RNA secondary structures
RNAduplex	Compute the structure upon hybridization of two RNA strands
RNAeval	Evaluate free energy of RNA sequences with given secondary structure
RNAfold	Calculate minimum free energy secondary structures and partition function of RNAs
RNAforester	Compare RNA secondary structures via forest alignment
RNAheat	Calculate the specific heat (melting curve) of an RNA sequence
RNAinverse	Find RNA sequences with given secondary structure (sequence design)
RNALalifold	Calculate locally stable secondary structures for a set of aligned RNAs
RNALfold	Calculate locally stable secondary structures of long RNAs
RNApaln	RNA alignment based on sequence base pairing propensities
RNApdist	Calculate distances between thermodynamic RNA secondary structures ensembles
RNAparconv	Convert energy parameter files from ViennaRNA 1.8 to 2.0 format
RNAPKplex	Predict RNA secondary structures including pseudoknots
RNAplex	Find targets of a query RNA
RNAplfold	Calculate average pair probabilities for locally stable secondary structures
RNAplot	Draw RNA Secondary Structures in PostScript, SVG, or GML
RNAsnoop	Find targets of a query H/ACA snoRNA
RNAsubopt	Calculate suboptimal secondary structures of RNAs
RNAup	Calculate the thermodynamics of RNA-RNA interactions

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References

1 2 Hofacker, I. L.; Fontana, W.; Stadler, P. F.; Bonhoeffer, L. S.; Tacker, M.; Schuster, P. (1994-02-01). "Fast folding and comparison of RNA secondary structures". Monatshefte für Chemie. 125 (2): 167–188. doi:10.1007/BF00818163. ISSN 0026-9247. S2CID 19344304.
↑ Vella, F. (1992). "Introduction to Protein Structure". Biochemical Education. 20 (2): 122. doi:10.1016/0307-4412(92)90132-6.
↑ Whisstock, James C.; Lesk, Arthur M. (2003-08-01). "Prediction of protein function from protein sequence and structure". Quarterly Reviews of Biophysics. 36 (3): 307–340. doi:10.1017/S0033583503003901. ISSN 1469-8994. PMID 15029827. S2CID 27123114.
↑ Lee, David; Redfern, Oliver; Orengo, Christine (2007). "Predicting protein function from sequence and structure". Nature Reviews Molecular Cell Biology. 8 (12): 995–1005. doi:10.1038/nrm2281. PMID 18037900. S2CID 14432468.
↑ Mathews, David H.; Disney, Matthew D.; Childs, Jessica L.; Schroeder, Susan J.; Zuker, Michael; Turner, Douglas H. (2004-05-11). "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure". Proceedings of the National Academy of Sciences of the United States of America. 101 (19): 7287–7292. Bibcode:2004PNAS..101.7287M. doi: 10.1073/pnas.0401799101 . ISSN 0027-8424. PMC 409911 . PMID 15123812.
↑ Lorenz, Ronny; Bernhart, Stephan H; Siederdissen, Christian Höner zu; Tafer, Hakim; Flamm, Christoph; Stadler, Peter F; Hofacker, Ivo L (2011-11-24). "ViennaRNA Package 2.0". Algorithms for Molecular Biology. 6 (1): 26. doi: 10.1186/1748-7188-6-26 . PMC 3319429 . PMID 22115189.
↑ Gruber, Andreas R.; Lorenz, Ronny; Bernhart, Stephan H.; Neuböck, Richard; Hofacker, Ivo L. (2008-07-01). "The Vienna RNA Websuite". Nucleic Acids Research. 36 (suppl 2): W70–W74. doi:10.1093/nar/gkn188. ISSN 0305-1048. PMC 2447809 . PMID 18424795.
↑ Hofacker, Ivo L. (2003-07-01). "Vienna RNA secondary structure server". Nucleic Acids Research. 31 (13): 3429–3431. doi:10.1093/nar/gkg599. ISSN 0305-1048. PMC 169005 . PMID 12824340.
↑ "TBI - ViennaRNA Package 2". www.tbi.univie.ac.at. Retrieved 2016-01-11.