Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

RNAstructure: Software for RNA Secondary Structure Prediction and Analysis

RNAstructure is a software package for RNA secondary structure prediction and analysis. It predicts lowest free energy structures and low free energy structures either by using a heuristic or by determining all possible low free energy structures. These calculations can be performed for unimolecular secondary structures or for bimolecular secondary structures. Stochastic sampling of secondary structures from the Boltzmann ensemble is also implemented. Base pair probabilities are predicted using a partition function. For these structure prediction methods, facilities are included for utilizing mapping data from wet lab experiments, including enzymatic cleavage, chemical modification, and SHAPE. For a given RNA target, regions accessible to hybridization can be predicted. This is important for antisense deoxynucleotide or siRNA design. Secondary structures common to two sequences can be predicted using the Dynalign algorithm. Finally, a tool for removing pseudoknots is included. The latest nearest neighbor parameters for RNA, DNA, and RNA-DNA hybrids are utilized.

RNAstructure has been distributed with a graphical user interface (GUI) for Microsoft Windows and is known to function with the Linux Windows Emulator (WINE). Here we report significant expansions to the package to address portability. A new JAVA GUI has been designed and implemented. Executables are now provided for using this GUI in Windows, Linux, or Macintosh OS X. This GUI is linked to the C++ backend code using SWIG. Furthermore, text interfaces are provided to each component and these are available with standard Unix Makefiles, allowing local compilation and use of the tools. The tools are tested and known to run with the Linux GNU compiler, Linux Intel C compiler, Cygwin GNU compiler, Intel C compiler for Windows, and Macintosh OS X GNU compiler. Finally, a new object-oriented library of tools is made available. This compiles as a shared library that can be linked into C++ programs.

The new interfaces added to the RNAstructure package allow it to be used by a wider audience. It also will improve its utility by making the functions available to developers.

Jessica Reuter
David H. Mathews

Department of Biochemistry & Biophysics
University of Rochester Medical Center
601 Elmwood Avenue, Box 712
Rochester, NY 14642

Phone: 585-286-4337
Fax: 585-275-6007
email: Jessica Reuter