RNAstructure: software for RNA secondary structure prediction and analysis

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.

Figure 1

Class inheritance diagram. The four main classes that provide functionality, named in boldface, are RNA, Oligowalk_object, HybridRNA, and Dynalign_object. Solid lines show inheritance and the dotted lines indicate that a class contains an instance of another. TwoRNA contains two instances of RNA and HybridRNA contains an instance of TwoRNA.

Figure 2

A screenshot of the JAVA GUI for predicting the lowest free energy structure for sequence "pcarinii.seq".

Figure 3

A screenshot of the JAVA GUI displaying the predicted lowest free energy structure for the sequence input as shown in Figure 2.