NOTE: Due to lack of use, the ViennaRNA software module has been disabled and will be removed from MSI systems on 8/10/2017. If you need this software, please contact firstname.lastname@example.org.
The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
module load viennarna
For a detailed information, take a look at the HTML versions of the man pages for the programs at http://www.tbi.univie.ac.at/RNA/.
- RNAfold -- predict minimum energy secondary structures and pair probabilities
- RNAeval -- evaluate energy of RNA secondary structures
- RNAheat -- calculate the specific heat (melting curve) of an RNA sequence
- RNAinverse -- inverse fold (design) sequences with predefined structure
- RNAdistance -- compare secondary structures
- RNApdist -- compare base pair probabilities
- RNAsubopt -- complete suboptimal folding
- RNAplot -- RNA structure drawings in PostScript, SVG, or GML
- RNAcofold -- predict hybrid structure of two sequences
- RNAduplex -- predict possible hybridization sites between two sequences
- RNAup -- predict RNA-RNA interaction sites using accessibilities
- RNAalifold -- predict the consensus structure of several aligned sequences
- RNAaliduplex -- comparative (multiple alignment) version of RNAduplex
- RNALfold -- predict locally stable structure of long sequences
- RNAplfold -- compute average pair probabilities for local base pairs in long sequences
- RNApaln -- fast structural alignment of RNA sequences using string alignments
- Several small but helpful Perl Utilities