The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
RNAstructure: software for RNA secondary structure prediction and analysis
Open accessAbstract
BACKGROUND: To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence. RESULTS: RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained. CONCLUSION: The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html.
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Cites
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
Self-citationGilbert, W. (1986) · Nature · doi:10.1038/319618a0 · Cited by 2,721
Predicting DNA duplex stability from the base sequence
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The chemical repertoire of natural ribozymes
Doudna, J. A., & Cech, T. R. (2002) · Nature · doi:10.1038/418222a · Cited by 745
Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes
Sugimoto, N., Nakano, S.-I., Katoh, M., Matsumura, A., Nakamuta, H., Ohmichi, T., Yoneyama, M., & Sasaki, M. (1995) · Biochemistry · doi:10.1021/bi00035a029 · Cited by 697 · cited 2×
“DNA-RNA hybridization parameters are also used by OligoWalk [93].”
MethodThermodynamics and NMR of Internal G·T Mismatches in DNA
Allawi, H. T., & SantaLucia, J. (1997) · Biochemistry · doi:10.1021/bi962590c · Cited by 623 · cited 1×
“For DNA, the parameters are derived from the experimental literature [56-92].”
MethodThe accuracy of ribosomal RNA comparative structure models
Gutell, R. R., Lee, J. C., & Cannone, J. J. (2002) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(02)00339-1 · Cited by 364
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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
In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
Ding, Y., Tang, Y., Kwok, C. K., Zhang, Y., Bevilacqua, P. C., & Assmann, S. M. (2014) · Nature · doi:10.1038/nature12756 · Cited by 775
A transfer-RNA-derived small RNA regulates ribosome biogenesis
Kim, H. K., Fuchs, G., Wang, S., Wei, W., Zhang, Y., Park, H., Roy-Chaudhuri, B., Li, P., Xu, J., Chu, K., et al. (2017) · Nature · doi:10.1038/nature25005 · Cited by 574
The Role of m6A/m-RNA Methylation in Stress Response Regulation
Engel, M., Eggert, C., Kaplick, P. M., Eder, M., Röh, S., Tietze, L., Namendorf, C., Arloth, J., Weber, P., Rex-Haffner, M., et al. (2018) · Neuron · doi:10.1016/j.neuron.2018.07.009 · Cited by 411
Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
Leppek, K., Byeon, G. W., Kladwang, W., Wayment-Steele, H. K., Kerr, C. H., Xu, A. F., Kim, D. S., Topkar, V. V., Choe, C., Rothschild, D., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28776-w · Cited by 399
Metadata
- Authors
- Reuter, J. S., & Mathews, D. H.
- Venue
- BMC Bioinformatics
- Published
- 2010-03-15
- Volume
- 11
- Issue
- 1
- Pages
- 129-129
- ISSN
- 1471-2105 (ISSN-L)
- OpenAlex
- W2098571862
- Cited by
- 2,012
- References
- 9
- FWCI
- 21.86
- Type
- journal article
- Language
- en
- Open access
- gold
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