Pfold

Knudsen, B.; Hein, J. J.: Pfold: RNA secondary structure prediction using stochastic context-free grammars. RNA secondary structures are important in many biological processes and efficient structure prediction can give vital directions for experimental investigations. Many available programs for RNA secondary structure prediction only use a single sequence at a time. This may be sufficient in some applications, but often it is possible to obtain related RNA sequences with conserved secondary structure. These should be included in structural analyses to give improved results. This work presents a practical way of predicting RNA secondary structure that is especially useful when related sequences can be obtained. The method improves a previous algorithm based on an explicit evolutionary model and a probabilistic model of structures. Predictions can be done on a web server at http://www.daimi.au.dk/ compbio/pfold


References in zbMATH (referenced in 12 articles , 1 standard article )

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  1. Cuesta, Jose A.; Manrubia, Susanna: Enumerating secondary structures and structural moieties for circular RNAs (2017)
  2. Huang, Fenix W. D.; Reidys, Christian M.: Topological language for RNA (2016)
  3. Fusy, Éric; Clote, Peter: Combinatorics of locally optimal RNA secondary structures (2014)
  4. Poznanović, Svetlana; Heitsch, Christine E.: Asymptotic distribution of motifs in a stochastic context-free grammar model of RNA folding (2014)
  5. Clote, Peter; Kranakis, Evangelos; Krizanc, Danny: Asymptotic number of hairpins of saturated RNA secondary structures (2013)
  6. Clote, Peter; Dobrev, Stefan; Dotu, Ivan; Kranakis, Evangelos; Krizanc, Danny; Urrutia, Jorge: On the page number of RNA secondary structures with pseudoknots (2012)
  7. Fang, Xiao-Yong; Luo, Zhi-Gang; Wang, Zheng-Hua: Predicting RNA secondary structure using profile stochastic context-free grammars and phylogenic analysis (2008) ioport
  8. Machado-Lima, Ariane; del Portillo, Hernando A.; Durham, Alan Mitchell: Computational methods in noncoding RNA research (2008)
  9. Zhao, Jizhen; Malmberg, Russell L.; Cai, Liming: Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition (2008)
  10. Brejová, Broňa; Brown, Daniel G.; Vinař, Tomáš: The most probable annotation problem in HMMs and its application to bioinformatics (2007)
  11. Knudsen, B.; Andersen, E. S.; Damgaard, C.; Kjems, J.; Gorodkin, J.: Evolutionary rate variation and RNA secondary structure prediction (2004)
  12. Knudsen, Bjarne; Hein, Jotun: Pfold: RNA secondary structure prediction using stochastic context-free grammars. (2003) ioport