Publications - Published papers
Please find below publications of our group. Currently, we list 565 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (
) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:
) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.
ViennaRNA Package 2.0
Ronny Lorenz, Stephan H Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler , Ivo L Hofacker
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Status: Published
Algorithms for Molecular Biology 2011, 6:26
Abstract
Background: Secondary structure forms an important intermediate level of description of nucleic acids that
encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely used
as a basis to explain experimental findings. Based on carefully measured thermodynamic parameters, exact
dynamic programming algorithms can be used to compute ground states, base pairing probabilities, as well as
thermodynamic properties.<br/>
Results: The ViennaRNA Package has been a widely used compilation of RNA secondary structure related
computer programs for nearly two decades. Major changes in the structure of the standard energy model, the
Turner 2004 parameters, the pervasive use of multi-core CPUs, and an increasing number of algorithmic
variants prompted a major technical overhaul of both the underlying RNAlib and the interactive user programs.
New features include an expanded repertoire of tools to assess RNA-RNA interactions and restricted ensembles
of structures, 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. Updates were implemented without compromising the computational efficiency of
the core algorithms and ensuring compatibility with earlier versions.<br/>
Conclusions: The ViennaRNA Package 2.0, supporting concurrent computations via OpenMP, can be
downloaded from www.tbi.univie.ac.at/RNA.