RNAstructure, Version 6.0:

updated 9/21/2017

RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data.

RNAstructure is available as a graphical user interface for Windows; a JAVA graphical user interface for Mac OS-X or Linux; command line interfaces for Max OS-X, Linux, or Windows; and source code for local compilation. The source code includes a set of C++ classes for convenient inclusion of the methods into new programs.

A complete list of components of the package can be found here.


We ask you to register before downloading so that we may occasionally notify you of significant updates and to track the number of users to make a case for continued support by funding agencies. RNAstructure is free of charge and provided under the GNU public license.

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Grant Support:

RNAstructure was made possible by the support of the National Institutes of Health grant R01GM076485.