path: root/academic/ViennaRNA/README

# ViennaRNA Package

A C code library and several stand-alone programs for the prediction
and comparison of RNA secondary structures.

A recent addition, RNAxplorer, requires lapacke (which requires
lapack that depends on a version of blas). During configuration the
step for RNAxplorer stalls (on missing lapack) because it does not
find the version of blas that has been used for compiling lapack
(see https://github.com/ViennaRNA/ViennaRNA/issues/206).
An extra variable ($BLAS) in the SlackBuild sets openblas as the
version of blas used for lapack(e). Please, adjust  $BLAS to the blas
used on your system.

A tutorial (see /usr/doc/$PRGNAM-$VERSION/RNA-tutorial-$VERSION.pdf)
and examples can be found in /usr/share/$PRGNAM/tutorial and
/usr/share/$PRGNAM/examples

For those who wish to link the Vienna package to their own C, perl
or python programs (see below), the RNAlib Reference Manual can be
assessed at:

https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/index.html
(or unpacked from the src: $PRGNAM-$VERSION/doc/html/)
https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/RNAlib-$VERSION.pdf
(or unpacked from the src: $PRGNAM-$VERSION/doc/RNAlib-$VERSION.pdf)

Amongst other things, the ViennRNA implementations allow you to:

- predict minimum free energy secondary structures
- calculate the partition function for the ensemble of structures
- compute various equilibrium probabilities
- calculate suboptimal structures in a given energy range
- compute local structures in long sequences
- predict consensus secondary structures from a multiple sequence
  alignment
- predict melting curves
- search for sequences folding into a given structure
- compare two secondary structures
- predict hybridization structures of two RNA molecules

The package includes `Perl` and `Python 3` modules that give access
to almost all functions of the C library from within the respective
scripting languages.

For further/most recent info see:

https://www.tbi.univie.ac.at/RNA/documentation.html