The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. RNA secondary structure prediction through energy minimization is the most used function in the package. It includes three kinds of dynamic programming algorithms for structure prediction: the minimum free energy algorithm of (Zuker & Stiegler 1981) which yields a single optimal structure, the partition function algorithm of (McCaskill 1990) which calculates base pair probabilities in the thermodynamic ensemble, and the suboptimal folding algorithm of (Wuchty et.al 1999) which generates all suboptimal structures within a given energy range of the optimal energy. For secondary structure comparison, the package contains several measures of distance (dissimilarities) using either string alignment or tree-editing (Shapiro & Zhang 1990). Finally, it includes an algorithm to design sequences with a predefined structure (inverse folding).

ViennaRNA was developed at the Institut für theoretische Chemie, Austria.

The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.

$ module avail viennarna
-------------------- /usr/local/Modules/3.2.9/modulefiles ----------------------
viennarna/1.8.5          viennarna/2.0.2          viennarna/2.1.1(default)

$ module load viennarna

$ module list
Currently Loaded Modulefiles:
  1) viennarna/2.1.1

$ module unload viennarna

$ module load viennarna/1.8.5

$ module show viennarna
-------------------------------------------------------------------
/usr/local/Modules/3.2.9/modulefiles/viennarna/2.1.1:

module-whatis    Sets up ViennaRNA 2.1.1 
prepend-path     PATH /usr/local/apps/viennarna/2.1.1/bin 
-----------------------------------------------------------------

Sample session using the RNAfold command from the ViennaRNA package:

http://www.tbi.univie.ac.at/~ivo/RNA/index.html