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The ViennaRNA 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 & 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).
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