Secondary Structure Prediction of Single Sequences Using RNAstructure.
RNA secondary structure is often predicted using folding thermodynamics. RNAstructure is a software package that includes structure prediction by free energy minimization, prediction of base pairing probabilities, prediction of structures composed of highly probably base pairs, and prediction of structures with pseudoknots. A user-friendly graphical user interface is provided, and this interface works on Windows, Apple OS X, and Linux. This chapter provides protocols for using RNAstructure for structure prediction.
Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA.|Department of Biochemistry & Biophysics, Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA.
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Department of Biochemistry & Biophysics, Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA. David_Mathews@urmc.rochester.edu.
David H
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D008958:Models, Molecular; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding; D012984:Software; D013816:Thermodynamics; D014584:User-Computer Interface; D064878:Web Browser
D012313:RNA
RNA folding thermodynamics; RNA statistical mechanics; RNA structure prediction