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Signed-off-by: B. Watson <yalhcru@gmail.com> Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
54 lines
2.2 KiB
Text
54 lines
2.2 KiB
Text
# ViennaRNA Package
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A C code library and several stand-alone programs for the prediction
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and comparison of RNA secondary structures.
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A tutorial (see /usr/doc/$PRGNAM-$VERSION/RNA-tutorial-$VERSION.pdf)
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and examples can be found in /usr/share/$PRGNAM/tutorial and
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/usr/share/$PRGNAM/examples
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For those who wish to link the Vienna package to their own C, perl
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or python programs (see below), the RNAlib Reference Manual can be
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assessed at:
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https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/index.html
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(or unpacked from the src: $PRGNAM-$VERSION/doc/html/)
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https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/RNAlib-$VERSION.pdf
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(or unpacked from the src: $PRGNAM-$VERSION/doc/RNAlib-$VERSION.pdf)
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Amongst other things, the ViennRNA implementations allow you to:
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- predict minimum free energy secondary structures
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- calculate the partition function for the ensemble of structures
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- compute various equilibrium probabilities
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- calculate suboptimal structures in a given energy range
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- compute local structures in long sequences
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- predict consensus secondary structures from a multiple sequence
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alignment
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- predict melting curves
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- search for sequences folding into a given structure
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- compare two secondary structures
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- predict hybridization structures of two RNA molecules
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The package includes `Perl 5` and `Python 3` modules that give access
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to almost all functions of the C library from within the respective
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scripting languages. For this reason, python3 is a dependency
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The `Python 2` module can be built as well, or instead of the one
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for `Python 3`; just edit the SlackBuild or run it by setting build
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options PYTHON=yes PYTHON3=no. (e.g. in sbopkg or run it from
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the commandline -within the directory containing the SlackBuild
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script and downloaded source archive- as: `PYTHON=yes PYTHON3=no
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./ViennaRNA.SlackBuild`)
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There is also a set of programs for analyzing sequence and distance
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data using split decomposition, statistical geometry, and cluster
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methods. They are not maintained any more and not built by default.
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The code very rarely uses static arrays, and all programs should work
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for sequences up to a length of 32,700 (if you have huge amounts of
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memory that is).
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For further info see:
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https://www.tbi.univie.ac.at/RNA/documentation.html
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