ViennaRNA Package 2.0

Algorithms for Molecular Biology : AMB
Ronny LorenzIvo L Hofacker

Abstract

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. 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 witho...Continue Reading

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Citations

Sep 13, 2013·Nature Communications·Klas Hatje, Martin Kollmar
Jan 22, 2013·Nature Methods·Mohsen KhorshidErik van Nimwegen
Jul 26, 2012·Bioinformatics·Ronny LorenzStephan H Bernhart
Jun 6, 2013·Bioinformatics·Orion J BuskeMichael Brudno
Aug 27, 2013·Bioinformatics·Nikolai HeckerAndrew E Torda
Sep 21, 2013·Bioinformatics·Thomas SchnattingerHans A Kestler
Jan 1, 2013·Nucleic Acids Research·Manja WachsmuthMario Mörl
Jan 18, 2013·Nucleic Acids Research·Paulo GasparJosé Luís Oliveira
Mar 21, 2013·Nucleic Acids Research·Jeff R Proctor, Irmtraud M Meyer
Apr 30, 2013·Nucleic Acids Research·Jing Yun A ZhuIrmtraud M Meyer
Jun 12, 2013·Nucleic Acids Research·Yang ZhangJérôme Waldispühl
Jan 5, 2013·Science·Prashant MaliGeorge M Church
Oct 12, 2013·Science·P V MaillardOlivier Voinnet
Jul 10, 2013·Microbial Cell Factories·Sang Jun LeeDong Gyun Kim
Nov 5, 2013·Algorithms for Molecular Biology : AMB·Harry A Stern, David H Mathews
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Feb 20, 2014·Molecular Therapy. Nucleic Acids·Lykke PedersenMorten Lindow
Feb 25, 2014·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Yang DingPeter Clote

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Software Mentioned

mfe
Vienna
RNAsnoop
INFO
RNAsalsa
RNAcofold
RNAparconv
RNAPKplex
ViennaRNA Package
McCaskill

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