Viennarna

Introduction

Viennarna is a set of standalone programs and libraries used for prediction and analysis of RNA secondary structures.

For more information, please check its website: https://biocontainers.pro/tools/viennarna and its home page: https://www.tbi.univie.ac.at/RNA/.

Versions

  • 2.5.0

Commands

  • RNA2Dfold

  • RNALalifold

  • RNALfold

  • RNAPKplex

  • RNAaliduplex

  • RNAalifold

  • RNAcofold

  • RNAdistance

  • RNAdos

  • RNAduplex

  • RNAeval

  • RNAfold

  • RNAforester

  • RNAheat

  • RNAinverse

  • RNAlocmin

  • RNAmultifold

  • RNApaln

  • RNAparconv

  • RNApdist

  • RNAplex

  • RNAplfold

  • RNAplot

  • RNApvmin

  • RNAsnoop

  • RNAsubopt

  • RNAup

  • Kinfold

  • b2ct

  • popt

Module

You can load the modules by:

module load biocontainers
module load viennarna

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Viennarna on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=viennarna
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers viennarna

RNAfold < test.seq
RNAfold -p --MEA < test.seq