ViennaRNA

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).


References in zbMATH (referenced in 20 articles , 1 standard article )

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  1. Clote, P.: Are RNA networks scale-free? (2020)
  2. Willmott, Devin; Murrugarra, David; Ye, Qiang: Improving RNA secondary structure prediction via state inference with deep recurrent neural networks (2020)
  3. Clote, Peter; Bayegan, Amir H.: RNA folding kinetics using Monte Carlo and Gillespie algorithms (2018)
  4. Li, Thomas J. X.; Reidys, Christian M.: The rainbow spectrum of RNA secondary structures (2018)
  5. Walter Costa, Maria Beatriz; Höner zu Siederdissen, Christian; Tulpan, Dan; Stadler, Peter F.; Nowick, Katja: Temporal ordering of substitutions in RNA evolution: uncovering the structural evolution of the Human Accelerated Region 1 (2018)
  6. Bayegan, Amir H.; Clote, Peter: An IP algorithm for RNA folding trajectories (2017)
  7. Berkemer, Sarah J.; Höner zu Siederdissen, Christian; Stadler, Peter F.: Algebraic dynamic programming on trees (2017)
  8. Keith, Jonathan M. (ed.): Bioinformatics. Volume II: structure, function, and applications (2017)
  9. Ota, Makoto; Seki, Shinnosuke: Rule set design problems for oritatami systems (2017)
  10. Fellermann, Harold; Lopiccolo, Annunziata; Kozyra, Jerzy; Krasnogor, Natalio: In vitro implementation of a stack data structure based on DNA strand displacement (2016)
  11. 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)
  12. Riechert, Maik; Höner zu Siederdissen, Christian; Stadler, Peter F.: Algebraic dynamic programming for multiple context-free grammars (2016)
  13. Picardi, Ernesto (ed.): RNA bioinformatics (2015)
  14. Clote, Peter; Ponty, Yann; Steyaert, Jean-Marc: Expected distance between terminal nucleotides of RNA secondary structures (2012)
  15. Sumedha; Martin, Olivier C.; Peliti, Luca: Population size effects in evolutionary dynamics on neutral networks and toy landscapes (2007)
  16. Kijima, Atsushi; Kobayashi, Satoshi: Efficient algorithm for testing structure freeness of finite set of biomolecular sequences (2006)
  17. Rodriguez, German; Badia, Rosa M.; Labarta, Jesús: Generation of simple analytical models for message passing applications (2004)
  18. Gabriel, Edgar; Keller, Rainer; Lindner, Peggy; Müller, Matthias S.; Resch, Michael M.: Software development in the grid: The DAMIEN tool-set (2003)
  19. Brenneman, Arwen; Condon, Anne: Strand design for biomolecular computation. (2002)
  20. Ruben, Adam J.; Freeland, Stephen J.; Landweber, Laura F.: PUNCH: An evolutionary algorithm for optimizing bit set selection (2002)