25 lines
1.3 KiB
XML
25 lines
1.3 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
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<pkgmetadata>
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<maintainer type="project">
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<email>sci-biology@gentoo.org</email>
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<name>Gentoo Biology Project</name>
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</maintainer>
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<longdescription>
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The Vienna RNA Package consists of a C code library and several
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stand-alone programs for the prediction and comparison of RNA secondary
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structures. RNA secondary structure prediction through energy
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minimization is the most used function in the package. We provide three
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kinds of dynamic programming algorithms for structure prediction: the
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minimum free energy algorithm of (Zuker and Stiegler 1981) which yields a
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single optimal structure, the partition function algorithm of
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(McCaskill 1990) which calculates base pair probabilities in the
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thermodynamic ensemble, and the suboptimal folding algorithm of
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(Wuchty et.al 1999) which generates all suboptimal structures within a
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given energy range of the optimal energy. For secondary structure
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comparison, the package contains several measures of distance
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(dissimilarities) using either string alignment or tree-editing
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(Shapiro and Zhang 1990). Finally, we provide an algorithm to design
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sequences with a predefined structure (inverse folding).
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</longdescription>
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</pkgmetadata>
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