Installed Vienna Package

We are installing version 1.6.1 of the Vienna RNA package.
The following tools will be available:
RNAheat -- calculate the specific heat (melting curve) of an RNA sequence
RNAfold -- predict minimum energy secondary structures and pair probabilities
RNAalifold -- predict the consensus structure of several aligned sequences

The official man page are available on the name's link. Papers and references can be found at http://www.tbi.univie.ac.at/papers/

Help for the Bioinformatica Vienna Package

The Help file is included in the tool, just click on the highlited links on top of each field and option menu.

What is it ?

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. The package provides 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, the package provides an algorithm to design sequences with a predefined structure (inverse folding).