The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Pfold: RNA secondary structure prediction using stochastic context-free grammars
Open accessAbstract
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.
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Cites
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Evolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032
Mathews, D. H., Sabina, J., Zuker, M., & Turner, D. H. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2700 · Cited by 3,795
[20] Computer prediction of RNA structure
Zuker, M. (1989) · Methods in Enzymology · doi:10.1016/0076-6879(89)80106-5 · Cited by 388 · cited 2×
“Zuker’s energy calculations have been further improved (9–11) and are probably the most widely used RNA secondary structure prediction method today (with the MFOLD program).”
Method
Cited by
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
Splicing mutations in human genetic disorders: Examples, detection, and confirmation
Anna, A., & Monika, G. (2018) · Journal of Applied Genetics · doi:10.1007/s13353-018-0444-7 · Cited by 657
Pijlman, G. P., Funk, A., Kondratieva, N., Leung, J., Torres, S., van der Aa, L., Liu, W. J., Palmenberg, A. C., Shi, P.-Y., Hall, R. A., et al. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.10.007 · Cited by 490
Weinberg, Z., Wang, J. X., Bogue, J., Yang, J., Corbino, K., Moy, R. H., & Breaker, R. R. (2010) · Genome Biology · doi:10.1186/gb-2010-11-3-r31 · Cited by 354
Sato, K., Kato, Y., Hamada, M., Akutsu, T., & Asai, K. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr215 · Cited by 331
Metadata
- Authors
- Knudsen, B., & Hein, J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2003-07-01
- Volume
- 31
- Issue
- 13
- Pages
- 3423-3428
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2137640371
- Cited by
- 456
- References
- 4
- FWCI
- 5.25
- Type
- journal article
- Language
- en
- Open access
- bronze
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