ViennaRNA Package 2.0 View Full Text


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Article Info

DATE

2011-11-24

AUTHORS

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

ABSTRACT

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

PAGES

26

References to SciGraph publications

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  • 2008-04-27. The impact of target site accessibility on the design of effective siRNAs in NATURE BIOTECHNOLOGY
  • 2004. The Partition Function Variant of Sankoff’s Algorithm in COMPUTATIONAL SCIENCE - ICCS 2004
  • 2008-08-13. RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database in BMC BIOINFORMATICS
  • 2008-11-11. RNAalifold: improved consensus structure prediction for RNA alignments in BMC BIOINFORMATICS
  • 2007-05-31. RNAstrand: reading direction of structured RNAs in multiple sequence alignments in ALGORITHMS FOR MOLECULAR BIOLOGY
  • 1984-07. RNA secondary structures and their prediction in BULLETIN OF MATHEMATICAL BIOLOGY
  • 2008. UNAFold in BIOINFORMATICS
  • 2006-01. Partition function and base pairing probabilities of RNA heterodimers in ALGORITHMS FOR MOLECULAR BIOLOGY
  • 1993-04. RNA multi-structure landscapes in EUROPEAN BIOPHYSICS JOURNAL
  • 2008-03. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data in NATURE
  • 2008-01-01. Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics in BIOINFORMATICS RESEARCH AND DEVELOPMENT
  • Journal

    TITLE

    Algorithms for Molecular Biology

    ISSUE

    1

    VOLUME

    6

    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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    31 schema:description BackgroundSecondary 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.ResultsThe 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.ConclusionsThe ViennaRNA Package 2.0, supporting concurrent computations via OpenMP, can be downloaded from http://www.tbi.univie.ac.at/RNA.
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