vienna-rna
RNA sequence analysis
Description
The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. It is developed and maintained by the group of Ivo Hofacker in Vienna. RNA secondary structure prediction through energy minimization is the most used function in the package. It 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, is provided an algorithm
to design sequences with a predefined structure (inverse folding).
The RNAforester package is a tool for aligning RNA secondary structures
and it's user interface integrates to those of the tools of the
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Homepage
https://www.tbi.univie.ac.at/RNA/
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