RNAstructure: Web servers for RNA secondary structure prediction and analysis

Abstract

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.

Figure 1.

Sample structure prediction. This is the predicted lowest free energy structure for the sample sequence for the ‘Predict a Secondary Structure’ server. This sequence is the tRNA RA7680 from the Sprinzl database (41). It is color annotated according to base pairing probability; more probable pairs are more likely to be correctly predicted than less probable pairs (30).