ViennaRNA Package
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.
| Original author(s) | Hofacker et al., |
|---|---|
| Developer(s) | Institut für theoretische Chemie, Währingerstr |
| Stable release | v2.4.17
/ 25 November 2020 |
| Written in | C, Perl |
| Operating system | Linux, macOS, Windows |
| Size | 13.4 MB (Source) |
| Type | Bioinformatics |
| Website | www |
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]
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 |
References
- 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. 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.