RNA Secondary Structure Prediction by Minimum Free Energy
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RNA Secondary Structure Prediction by Minimum Free Energy
RNA Secondary Structure Prediction Including Pseudoknots, Figure 2 RNA secondary structures illustrating restrictions of pseudoknot prediction algorithms. Backbone is drawn as a straight line while base pairings are shown with zigzagged arcs
Data Sets PseudoBase at http://biology.leidenuniv.nl/~batenburg/ PKB.html is a repository of representatives of most known RNA structures with pseudoknots.
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URL to Code
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The method of Theorem 3 is available at http://selab. janelia.org/software.html#pknots, of one of the methods of Theorem 5 at http://www.nupack.org, and an implementation applying a slight heuristic reduction of the class of structures considered by the method of Theorem 6 is available at http://bibiserv.techfak.uni-bielefeld. de/pknotsrg/ [10].
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Cross References
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RNA Secondary Structure Prediction by Minimum Free Energy
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Recommended Reading
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1. Akutsu, T.: Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots. Discret. Appl. Math. 104, 45–62 (2000) 2. Brown, M., Wilson, C.: RNA pseudoknot modeling using intersections of stochastic context free grammars with applications to database search. In: Hunter, L., Klein, T. (eds.) Proceedings of the 1st Pacific Symposium on Biocomputing, 1996, pp. 109– 125 3. Condon, A., Davy, B., Rastegari, B., Tarrant, F., Zhao, S.: Classifying RNA pseudoknotted structures. Theor. Comput. Sci. 320, 35–50 (2004) 4. Dirks, R.M., Pierce, N.A.: A partition function algorithm for nucleic acid secondary structure including pseudoknots. J. Comput. Chem. 24, 1664–1677 (2003) 5. Gluick, T.C., Draper, D.E.: Thermodynamics of folding a pseudoknotted mRNA fragment. J. Mol. Biol. 241, 246–262 (1994) 6. Ieong, S., Kao, M.-Y., Lam, T.-W., Sung, W.-K., Yiu, S.-M.: Predicting RNA secondary structures with arbitrary pseudoknots
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by maximizing the number of stacking pairs. In: Proceedings of the 2nd Symposium on Bioinformatics and Bioengineering, 2001, pp. 183–190 Lyngsø, R.B.: Complexity of pseudoknot prediction in simple models. In: Proceedings of the 31th International Colloquium on Automata, Languages and Programming (ICALP), 2004, pp. 919–931 Lyngsø, R.B., Pedersen, C.N.S.: RNA pseudoknot prediction in energy based models. J. Comput. Biol. 7, 409–428 (2000) Rastegari, B., Condon, A.: Parsing nucleic acid pseudoknotted secondary structure: algorithm and applications. J. Comput. Biol. 14(1), 16–32 (2007) Reeder, J., Giegerich, R.: Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinform. 5, 104 (2004) Rivas, E., Eddy, S.: A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol. 285, 2053–2068 (1999) Rødland, E.A.: Pseudoknots in RNA secondary structure: Representation, enumeration, and prevalence. J. Comput. Biol. 13, 1197–1213 (2006) Tabaska, J.E., Cary, R.B., Gabow, H.N., Stormo, G.D.: An RNA folding method capable of identifying pseudoknots and base triple
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