| ## RNAstructure GUI Help Introduction | ### Contents ### Index
### General Information The core of RNAstructure is a dynamic programming algorithm to predict RNA or DNA secondary structures from sequence based on the principle of minimizing free energy. The thermodynamic parameters used for RNA predictions are the latest available from the Turner laboratory. Several modules are provided to extend the capabilities of secondary structure prediction, including the prediction of a secondary structure common to two sequences, and to make this a user-friendly RNA folding program. RNAstructure was originally written by David H. Mathews for Isis Pharmaceuticals (now Ionis) and is made available for the RNA community by Isis. RNAstructure is now supported by U.S. National Institutes of Health grant R35GM145283 and was previously supported by R01GM076485. It is available on the Mathews Lab Homepage. Two other modern implementations of the dynamic programming algorithm for RNA secondary structure prediction are mfold/UNAfold, available on the World Wide Web at Michael Zuker's homepage, and the Vienna RNA package, maintained by Ivo Hofacker. The implementation of the thermodynamic parameters differs in multibranch and exterior loops, therefore some differences in the predicted lowest free energy structures are expected by different packages. Research benefitting from this program should cite the journal references on which this program is based (See "References"). ### Requirements RNAstructure can be run on Windows, Macintosh, or Linux systems. On Linux and Windows the program requires Java version 1.7 or higher. Oracle Java can be downloaded at: http://java.com/en/download/. The application bundle for Mac OS X includes the Java runtime, so it is not necessary to have Java installed on the system, but OS X 10.8.3 (Mountain Lion) or above is required. ### Contributors to Code David Mathews wrote the origal version of the GUI and now directs the project. Jessica Reuter wrote the Java interface. Richard Watson updated and maintains the JAVA interface. Many people contributed to the code that runs the calculations. A list of contributions can be found here. ### Special Thanks Thanks are deserved to those who helped with the creation and improvement of the program, including Marc Brower, Mark Burkard, Karina Burkard, Katie Deigan, Josh Diamond, Karim Fakhreddine, Sue Freier, Christine Hajdin, Arif Harmanci, Wayne Huggins, James Kim, Zhi John Lu, Olga Matveeva, Jeff McDowell, Jessica Reuter, Jeff Sabina, Gaurav Sharma, Steve Testa, Brent Townshend, Doug Turner, Rahul Tyagi, Kevin Weeks, Jacqueline Wyatt, and Michael Zuker.