ViennaRNA Package 2.0 View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2011-12

AUTHORS

Ronny Lorenz, Stephan H Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler, Ivo L Hofacker

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. 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. CONCLUSIONS: The ViennaRNA Package 2.0, supporting concurrent computations via OpenMP, can be downloaded from http://www.tbi.univie.ac.at/RNA. More... »

PAGES

26

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1748-7188-6-26

    DOI

    http://dx.doi.org/10.1186/1748-7188-6-26

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1046184001

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/22115189


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