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RNAstructure: software for RNA secondary structure prediction and analysis

Jessica S Reuter and David H Mathews*

Author Affiliations

Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA

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BMC Bioinformatics 2010, 11:129  doi:10.1186/1471-2105-11-129

Published: 15 March 2010

Abstract

Background

To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence.

Results

RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained.

Conclusion

The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html webcite.