|RNA secondary structure prediction through energy minimization is the most used function in the package. There are three kinds of dynamic programming algorithms for structure prediction provided: 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, we provide an algorithm to design sequences with a predefined structure (inverse folding).
hg clone https://toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnasubopt
|Minimum Galaxy Version
|Calculates suboptimal secondary structures of RNAs