The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
A dynamic programming algorithm for RNA structure prediction including pseudoknots 1 1Edited by I. Tinoco
Abstract
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of O(N6) in time and O(N4) in storage. The description of the algorithm is complex, which led us to adopt a useful graphical representation (Feynman diagrams) borrowed from quantum field theory. We present an implementation of the algorithm that generates the optimal minimum energy structure for a single RNA sequence, using standard RNA folding thermodynamic parameters augmented by a few parameters describing the thermodynamic stability of pseudoknots. We demonstrate the properties of the algorithm by using it to predict structures for several small pseudoknotted and non-pseudoknotted RNAs. Although the time and memory demands of the algorithm are steep, we believe this is the first algorithm to be able to fold optimal (minimum energy) pseudoknotted RNAs with the accepted RNA thermodynamic model.
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Citations
Cites
Gilbert, W. (1986) · Nature · doi:10.1038/319618a0 · Cited by 2,721
Improved free-energy parameters for predictions of RNA duplex stability.
Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T., & Turner, D. H. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.24.9373 · Cited by 1,470
[20] Computer prediction of RNA structure
Zuker, M. (1989) · Methods in Enzymology · doi:10.1016/0076-6879(89)80106-5 · Cited by 388 · cited 15×
“The Zuker algorithm (implemented in the programs MFOLD (Zuker, 1989a) and ViennaRNA (Schuster et al. , 1994)) is an efficient dynamic programming algorithm for identifying the globally minimal energy structure for a sequence, as defined by such a thermodynamic model (Zuker & Stiegler, 1981; Zuker &…”
MethodInfluential
Cited by
Fast and effective prediction of microRNA/target duplexes
REHMSMEIER, M., STEFFEN, P., HÖCHSMANN, M., & GIEGERICH, R. (2004) · RNA · doi:10.1261/rna.5248604 · Cited by 2,560
RNA Pseudoknot Prediction in Energy-Based Models
Lyngsø, R. B., & Pedersen, C. N. S. (2000) · Journal of Computational Biology · doi:10.1089/106652700750050862 · Cited by 359
Sato, K., Kato, Y., Hamada, M., Akutsu, T., & Asai, K. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr215 · Cited by 331
Rivas, E., & Eddy, S. R. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.7.583 · Cited by 279
Self-citationFontana, W. (2002) · BioEssays · doi:10.1002/bies.10190 · Cited by 179
Metadata
- Authors
- Rivas, E., & Eddy, S. R.
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 1999-02
- Volume
- 285
- Issue
- 5
- Pages
- 2053-2068
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W2123241418
- Cited by
- 754
- References
- 3
- Type
- book review
- Language
- en
- Open access
- closed
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- Rivas, E., & Eddy, S. R. (1999). A dynamic programming algorithm for RNA structure prediction including pseudoknots 1 1Edited by I. Tinoco. Journal of Molecular Biology. https://doi.org/10.1006/jmbi.1998.2436
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