ViennaRNA Package

The three dimensional structure of biological macromolecules like proteins and nucleic acids play a critical role in determining their functional role.{{Cite journal |title=Introduction to Protein Structure |journal=Biochemical Education |volume=20 |issue=2 |doi=10.1016/0307-4412(92)90132-6 |first=F. |last=Vella |pages=122 |year=1992}} This process of decoding function from the sequence is an experimentally and computationally challenging question addressed widely.{{Cite journal |title=Prediction of protein function from protein sequence and structure |journal=Quarterly Reviews of Biophysics |date=2003-08-01 |issn=1469-8994 |pages=307–340 |volume=36 |issue=3 |doi=10.1017/S0033583503003901 |first1=James C. |last1=Whisstock |first2=Arthur M. |last2=Lesk |pmid=15029827 |s2cid=27123114}}{{Cite journal |title=Predicting protein function from sequence and structure |journal=Nature Reviews Molecular Cell Biology |pages=995–1005 |volume=8 |issue=12 |doi=10.1038/nrm2281 |pmid=18037900 |first1=David |last1=Lee |first2=Oliver |last2=Redfern |first3=Christine |last3=Orengo |year=2007 |s2cid=14432468}} 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.

The first version of the ViennaRNA Package was published by Hofacker et al. in 1994. 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.

A number of major systemic changes were introduced in this version with the use of a new parametrized energy model (Turner 2004),{{Cite journal |title=Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure |journal=Proceedings of the National Academy of Sciences of the United States of America |date=2004-05-11 |issn=0027-8424 |pmc=409911 |pmid=15123812 |pages=7287–7292 |volume=101 |issue=19 |doi=10.1073/pnas.0401799101 |first1=David H. |last1=Mathews |first2=Matthew D. |last2=Disney |first3=Jessica L. |last3=Childs |first4=Susan J. |last4=Schroeder |first5=Michael |last5=Zuker |first6=Douglas H. |last6=Turner |bibcode=2004PNAS..101.7287M |doi-access=free}} 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.{{Cite journal |title=ViennaRNA Package 2.0 |journal=Algorithms for Molecular Biology |date=2011-11-24 |pmc=3319429 |pmid=22115189 |volume=6 |issue=1 |doi=10.1186/1748-7188-6-26 |first1=Ronny |last1=Lorenz |first2=Stephan H |last2=Bernhart |first3=Christian Höner zu |last3=Siederdissen |first4=Hakim |last4=Tafer |first5=Christoph |last5=Flamm |first6=Peter F |last6=Stadler |first7=Ivo L |last7=Hofacker |pages=26 |doi-access=free }}

The tools provided by the ViennaRNA Package are also available for public use through a web interface.{{Cite journal |title=The Vienna RNA Websuite |url= |journal=Nucleic Acids Research |date=2008-07-01 |issn=0305-1048 |pmc=2447809 |pmid=18424795 |pages=W70–W74 |volume=36 |issue=suppl 2 |doi=10.1093/nar/gkn188 |first1=Andreas R. |last1=Gruber |first2=Ronny |last2=Lorenz |first3=Stephan H. |last3=Bernhart |first4=Richard |last4=Neuböck |first5=Ivo L. |last5=Hofacker}}{{Cite journal |title=Vienna RNA secondary structure server |url= |journal=Nucleic Acids Research |date=2003-07-01 |issn=0305-1048 |pmid=12824340 |pages=3429–3431 |volume=31 |issue=13 |doi=10.1093/nar/gkg599 |first=Ivo L. |last=Hofacker |pmc=169005}}

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).{{Cite web |title=TBI - ViennaRNA Package 2 |url=http://www.tbi.univie.ac.at/RNA/documentation.html|website=www.tbi.univie.ac.at|access-date=2016-01-11}}

{{Reflist}}

• Nucleic acid structure determination
• Nucleic acid structure prediction
• List of RNA structure prediction software

• {{Official website|www.tbi.univie.ac.at/RNA}}
• {{GitHub|ViennaRNA}}

Category:Bioinformatics software

Category:Bioinformatics algorithms

Category:Computational biology