title: 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.
authors.affiliation: Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA.
authors.forename: Stanislav
authors.initials: S
authors.lastname: Bellaousov
authors.forename: Jessica S
authors.initials: JS
authors.lastname: Reuter
authors.forename: Matthew G
authors.initials: MG
authors.lastname: Seetin
authors.forename: David H
authors.initials: DH
authors.lastname: Mathews
mesh_terms: D020407:Internet; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012984:Software
chemical_list: D012313:RNA