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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
	<maintainer>
		<email>ribosome@gentoo.org</email>
		<name>Olivier Fisette</name>
	</maintainer>
	<herd>sci</herd>
	<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>