| <?xml version="1.0" encoding="UTF-8"?> |
| <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| <pkgmetadata> |
| <maintainer type="project"> |
| <email>sci-biology@gentoo.org</email> |
| <name>Gentoo Biology Project</name> |
| </maintainer> |
| <longdescription> |
| 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). |
| </longdescription> |
| </pkgmetadata> |