The DOI matches its Crossref record; 62 of the 62 references it cites were found in a registry or an index.
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction
Open accessAbstract
BACKGROUND: RNA secondary structure prediction methods based on probabilistic modeling can be developed using stochastic context-free grammars (SCFGs). Such methods can readily combine different sources of information that can be expressed probabilistically, such as an evolutionary model of comparative RNA sequence analysis and a biophysical model of structure plausibility. However, the number of free parameters in an integrated model for consensus RNA structure prediction can become untenable if the underlying SCFG design is too complex. Thus a key question is, what small, simple SCFG designs perform best for RNA secondary structure prediction? RESULTS: Nine different small SCFGs were implemented to explore the tradeoffs between model complexity and prediction accuracy. Each model was tested for single sequence structure prediction accuracy on a benchmark set of RNA secondary structures. CONCLUSIONS: Four SCFG designs had prediction accuracies near the performance of current energy minimization programs. One of these designs, introduced by Knudsen and Hein in their PFOLD algorithm, has only 21 free parameters and is significantly simpler than the others.
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Lorenz, R., Bernhart, S. H., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P. F., & Hofacker, I. L. (2011) · Algorithms for Molecular Biology · doi:10.1186/1748-7188-6-26 · Cited by 5,098
Accurate SHAPE-directed RNA structure determination
Deigan, K. E., Li, T. W., Mathews, D. H., & Weeks, K. M. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806929106 · Cited by 696
Comparing two K-category assignments by a K-category correlation coefficient
Gorodkin, J. (2004) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2004.09.006 · Cited by 545
Prediction of RNA secondary structure by free energy minimization
Mathews, D. H., & Turner, D. H. (2006) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2006.05.010 · Cited by 405
CENTROIDFOLD: a web server for RNA secondary structure prediction
Sato, K., Hamada, M., Asai, K., & Mituyama, T. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp367 · Cited by 334
Metadata
- Authors
- Dowell, R. D., & Eddy, S. R.
- Venue
- BMC Bioinformatics
- Published
- 2004-06-04
- Volume
- 5
- Issue
- 1
- Pages
- 71-71
- ISSN
- 1471-2105 (ISSN-L)
- OpenAlex
- W1861164398
- Cited by
- 280
- References
- 62
- FWCI
- 6.23
- Type
- journal article
- Language
- en
- Open access
- gold
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