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Methods Mol Biol. 2016;1490:15-34. doi: 10.1007/978-1-4939-6433-8_2.

Secondary Structure Prediction of Single Sequences Using RNAstructure.

Author information

1
Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA.
2
Department of Biochemistry & Biophysics, Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA.
3
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.

Abstract

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.

KEYWORDS:

RNA folding thermodynamics; RNA statistical mechanics; RNA structure prediction

PMID:
27665590
DOI:
10.1007/978-1-4939-6433-8_2
[Indexed for MEDLINE]

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