ViennaRNA swMATH ID: 10504 Software Authors: Lorenz, Ronny and Bernhart, Stephan H. and Höner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L. Description: The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. RNA secondary structure prediction through energy minimization is the most used function in the package. We provide three kinds of dynamic programming algorithms for structure prediction: the minimum free energy algorithm of (Zuker & Stiegler 1981) which yields a single optimal structure, the partition function algorithm of (McCaskill 1990) which calculates base pair probabilities in the thermodynamic ensemble, and the suboptimal folding algorithm of (Wuchty et.al 1999) which generates all suboptimal structures within a given energy range of the optimal energy. For secondary structure comparison, the package contains several measures of distance (dissimilarities) using either string alignment or tree-editing (Shapiro & Zhang 1990). Finally, we provide an algorithm to design sequences with a predefined structure (inverse folding). Homepage: http://www.tbi.univie.ac.at/RNA/ Related Software: Rfam; VARNA; NNDB; RNAsubopt; KEGG; Mfold; RNAstructure; UNAFold; PseudoViewer3; RNAfold; Infernal; FFTbor; PubChem; TopHat; Rnaz; BLAT; SynTReN; edgeR; Bioconductor; R Referenced in: 23 Publications Standard Articles 1 Publication describing the Software, including 1 Publication in zbMATH Year Expected distance between terminal nucleotides of RNA secondary structures. Zbl 1304.05073Clote, Peter; Ponty, Yann; Steyaert, Jean-Marc 2012 all top 5 Referenced by 51 Authors 4 Clote, Peter G. 3 Höner zu Siederdissen, Christian 3 Stadler, Peter F. 2 Bayegan, Amir H. 1 Akhlaghpour, Hessameddin 1 Badia, Rosa Maria 1 Bapat, Niraja V. 1 Berkemer, Sarah J. 1 Brenneman, Arwen 1 Condon, Anne E. 1 Derr, Julien 1 Elloumi, Mourad 1 Fellermann, Harold 1 Freeland, Stephen J. 1 Gabriel, Edgar 1 Greenwood, Torin 1 Heitsch, Christine E. 1 Jin, Emma Yu 1 Keith, Jonathan M. 1 Keller, Rainer 1 Kijima, Atsushi 1 Kobayashi, Satoshi 1 Kozyra, Jerzy 1 Krasnogor, Natalio 1 Labarta, Jesús 1 Landweber, Laura F. 1 Li, Thomas J. X. 1 Lindner, Peggy 1 Lopiccolo, Annunziata 1 Müller, Matthias S. 1 Murrugarra, David 1 Nebel, Markus E. 1 Nowick, Katja 1 Ota, Makoto 1 Picardi, Ernesto 1 Ponty, Yann 1 Rajamani, Sudha 1 Reidys, Christian Michael 1 Resch, Michael M. 1 Riechert, Maik 1 Rodriguez, German 1 Roy, Suvam 1 Ruben, Adam J. 1 Seki, Shinnosuke 1 Sengupta, Supratim 1 Steyaert, Jean-Marc 1 Tulpan, Dan C. 1 Walter Costa, Maria Beatriz 1 Willmott, Devin T. 1 Ye, Qiang 1 Zomaya, Albert Y. all top 5 Referenced in 7 Serials 4 Journal of Mathematical Biology 3 Theoretical Computer Science 3 Journal of Theoretical Biology 2 Bulletin of Mathematical Biology 2 Methods in Molecular Biology 1 Algorithms 1 Computational and Mathematical Biophysics all top 5 Referenced in 9 Fields 20 Biology and other natural sciences (92-XX) 12 Computer science (68-XX) 5 Operations research, mathematical programming (90-XX) 3 General and overarching topics; collections (00-XX) 3 Combinatorics (05-XX) 1 Calculus of variations and optimal control; optimization (49-XX) 1 Probability theory and stochastic processes (60-XX) 1 Statistics (62-XX) 1 Numerical analysis (65-XX) Referencing Publications by Year