sci-biology
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. We provide three
kinds of dynamic programming algorithms for structure prediction: the
minimum free energy algorithm of (Zuker and 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 and Zhang 1990). Finally, we provide an algorithm to design
sequences with a predefined structure (inverse folding).