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ViennaRNA Package

ViennaRNA Package
Original author(s)Hofacker et al.,
Developer(s)Institut für theoretische Chemie, Währingerstr
Initial release28 September 2000; 24 years ago (2000-09-28)
Stable release
2.6.4 / 25 September 2023; 14 months ago (2023-09-25)
Repositoryhttps://github.com/ViennaRNA/
Written inC, Perl, Python
Operating systemLinux, macOS, Windows
PlatformIA-32, x86-64
Size13.4 MB (source code)
Available inEnglish
TypeBioinformatics
LicenseFreeware
Websitewww.tbi.univie.ac.at/RNA

The ViennaRNA Package is software, a set of standalone programs and libraries used for predicting and analysing RNA nucleic acid secondary structures.[1] The source code for the package is released as free and open-source software and compiled binaries are available for the operating systems Linux, macOS, and Windows. The original paper has been cited over 2,000 times.

Background

The three dimensional structure of biological macromolecules like proteins and nucleic acids play a 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 partly 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. Many structure prediction tools have been implemented also.

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 application programming interface (API), and inclusion of several new auxiliary tools. For example, tools to assess RNA-RNA interactions and restricted ensembles of structures. Further, 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

References

  1. ^ a b Hofacker, I. L.; Fontana, W.; Stadler, P. F.; Bonhoeffer, L. S.; Tacker, M.; Schuster, P. (1 February 1994). "Fast folding and comparison of RNA secondary structures". Monatshefte für Chemie. 125 (2): 167–188. doi:10.1007/BF00818163. ISSN 0026-9247. S2CID 19344304.
  2. ^ Vella, F. (1992). "Introduction to Protein Structure". Biochemical Education. 20 (2): 122. doi:10.1016/0307-4412(92)90132-6.
  3. ^ Whisstock, James C.; Lesk, Arthur M. (1 August 2003). "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.
  4. ^ 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.
  5. ^ Mathews, David H.; Disney, Matthew D.; Childs, Jessica L.; Schroeder, Susan J.; Zuker, Michael; Turner, Douglas H. (11 May 2004). "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.
  6. ^ Lorenz, Ronny; Bernhart, Stephan H; Siederdissen, Christian Höner zu; Tafer, Hakim; Flamm, Christoph; Stadler, Peter F; Hofacker, Ivo L (24 November 2011). "ViennaRNA Package 2.0". Algorithms for Molecular Biology. 6 (1): 26. doi:10.1186/1748-7188-6-26. PMC 3319429. PMID 22115189.
  7. ^ Gruber, Andreas R.; Lorenz, Ronny; Bernhart, Stephan H.; Neuböck, Richard; Hofacker, Ivo L. (1 July 2008). "The Vienna RNA Websuite". Nucleic Acids Research. 36 (suppl 2): W70–W74. doi:10.1093/nar/gkn188. ISSN 0305-1048. PMC 2447809. PMID 18424795.
  8. ^ Hofacker, Ivo L. (1 July 2003). "Vienna RNA secondary structure server". Nucleic Acids Research. 31 (13): 3429–3431. doi:10.1093/nar/gkg599. ISSN 0305-1048. PMC 169005. PMID 12824340.
  9. ^ "TBI - ViennaRNA Package 2". www.tbi.univie.ac.at. Retrieved 11 January 2016.

See also

Quelle: https://en.wikipedia.org/wiki/ViennaRNA_Package