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48 lines
2 KiB
Text
48 lines
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 recent addition, RNAxplorer, requires lapacke (which requires
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lapack that depends on a version of blas). During configuration the
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step for RNAxplorer stalls (on missing lapack) because it does not
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find the version of blas that has been used for compiling lapack
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(see https://github.com/ViennaRNA/ViennaRNA/issues/206).
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An extra variable ($BLAS) in the SlackBuild sets openblas as the
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version of blas used for lapack(e). Please, adjust $BLAS to the blas
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used on your system.
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A tutorial (see /usr/doc/$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` 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.
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For further/most recent info see:
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https://www.tbi.univie.ac.at/RNA/documentation.html
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