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 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).

References in zbMATH (referenced in 11 articles , 1 standard article )

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  1. Clote, Peter; Bayegan, Amir H.: RNA folding kinetics using Monte Carlo and Gillespie algorithms (2018)
  2. Keith, Jonathan M. (ed.): Bioinformatics. Volume II: structure, function, and applications (2017)
  3. Ota, Makoto; Seki, Shinnosuke: Rule set design problems for oritatami systems (2017)
  4. Fellermann, Harold; Lopiccolo, Annunziata; Kozyra, Jerzy; Krasnogor, Natalio: In vitro implementation of a stack data structure based on DNA strand displacement (2016)
  5. Jin, Emma Yu; Nebel, Markus E.: RNA secondary structures in a polymer-zeta model how foldings should be shaped for sparsification to establish a linear speedup (2016)
  6. Riechert, Maik; Höner zu Siederdissen, Christian; Stadler, Peter F.: Algebraic dynamic programming for multiple context-free grammars (2016)
  7. Picardi, Ernesto (ed.): RNA bioinformatics (2015)
  8. Clote, Peter; Ponty, Yann; Steyaert, Jean-Marc: Expected distance between terminal nucleotides of RNA secondary structures (2012)
  9. Rodriguez, German; Badia, Rosa M.; Labarta, Jesús: Generation of simple analytical models for message passing applications (2004)
  10. Gabriel, Edgar; Keller, Rainer; Lindner, Peggy; Müller, Matthias S.; Resch, Michael M.: Software development in the grid: The DAMIEN tool-set (2003)
  11. Ruben, Adam J.; Freeland, Stephen J.; Landweber, Laura F.: PUNCH: An evolutionary algorithm for optimizing bit set selection (2002)