RNAstructure: web servers for RNA secondary structure prediction and analysis

By Stanislav Bellaousov, Jessica S. Reuter, Matthew G. Seetin, D. Mathews. Nucleic Acids Res., 2013

384 citations recorded by the source corpus.

RNAstructure is a software package for RNA secondary structure prediction and analysis. This contribution describes a new set of web servers to provide its functionality. The web server offers RNA secondary structure prediction, including free energy minimization, maximum expected accuracy structure prediction and pseudoknot prediction. Bimolecular secondary structure prediction is also provided. Additionally, the server can predict secondary structures conserved in either two homologs or more than two homologs. Folding free energy changes can be predicted for a given RNA structure using nearest neighbor rules. Secondary structures can be compared using circular plots or the scoring methods, sensitivity and positive predictive value. Additionally, structure drawings can be rendered as SVG, postscript, jpeg or pdf. The web server is freely available for public use at: http://rna.urmc.rochester.edu/RNAstructureWeb.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b936071e7a9110fadd16249ccd7585343cfd5e82

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In Materials Chemistry

1. Xin Gao
2. Ramzan Umarov
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4. Yu Li

In Molecular Biology

1. Xin Gao
2. Yu Li
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Citations in the corpus

• RNA Secondary Structure Prediction By Learning Unrolled Algorithms (2020, methodology): “A few widely used methods such as RNAstructure (Bellaousov et al., 2013), Vienna RNAfold (Lorenz et al., 2011) and UNAFold (Markham & Zuker, 2008) (Bellaousov & Mathews, 2010) have been made to predict structures with pseudoknots, but the predictive accuracy and efficiency still need to be improved.”