BiBiServ2 - RNAshapes

RNAshapes

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Janssen, Stefan and Giegerich, Robert The RNA shapes studio, Bioinformatics, 2015
Giegerich, Robert and Voss, Bjoern and Rehmsmeier, Marc Abstract Shapes of RNA, Nucleic Acids Research, 2004
Lorenz, Ronny and Bernhart, Stephan H and Hoener zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F and Hofacker, Ivo L ViennaRNA Package 2.0, Algorithms Molecular Biology, 2011
Gruber, Andreas R and Lorenz, Ronny and Bernhart, Stephan H and Neuboeck, Richard and Hofacker, Ivo L The Vienna RNA Websuite, Nucleic Acids Research, 2008
Mathews, David H. and Disney, Matthew D. and Childs, Jessica L. and Schroeder, Susan J. and Zuker, Michael and Turner, Douglas H. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure, Proceedings of the National Academy of Sciences of the United States of America, 2004
Turner, Douglas H. and Mathews, David H. NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure, Nucleic Acids Research, 2010
Janssen, Stefan and Schudoma, Christian and Steger, Gerhard and Giegerich, Robert Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction, BMC Bioinformatics, 2011
Janssen, Stefan and Giegerich, Robert Faster computation of exact RNA shape probabilities, Bioinformatics, 2010
Voss, Bjoern and Giegerich, Robert and Rehmsmeier, Marc Complete probabilistic analysis of RNA shapes, BMC Biology, 2006
Reeder, Jens and Giegerich, Robert Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction, Bioinformatics, 2005
Steffen, Peter and Voss, Bjoern and Rehmsmeier, Marc and Reeder, Jens and Giegerich, Robert RNAshapes: an integrated RNA analysis package based on abstract shapes, Bioinformatics, 2006
McCaskill and S., John The Equilibrium Partition Function and Base Pair Binding Probabilities for RNA Secondary Structure., Biopolymers, 1990
Weeks and M., Kevin Advances in RNA Secondary and Tertiary Structure Analysis by Chemical Probing., Current Opinion in Structural Biology, 2010
Deigan, Katherine E. and Li, Tian W. and Mathews, David H. and Weeks, Kevin M. Accurate SHAPE-directed RNA structure determination., Proceedings of the National Academy of Sciences, 2009
Saule, Cedric and Giegerich, Robert Pareto optimization in algebraic dynamic programming., Algorithms for Molecular Biology, 2015