Viennarna

Introduction

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

Versions

• 2.5.0

Commands

• b2ct

• Kinfold

• popt

• RNA2Dfold

• RNAaliduplex

• RNAalifold

• RNAcofold

• RNAdistance

• RNAdos

• RNAduplex

• RNAeval

• RNAfold

• RNAforester

• RNAheat

• RNAinverse

• RNALalifold

• RNALfold

• RNAlocmin

• RNAmultifold

• RNApaln

• RNAparconv

• RNApdist

• RNAPKplex

• RNAplex

• RNAplfold

• RNAplot

• RNApvmin

• RNAsnoop

• RNAsubopt

• RNAup

Example job

Adjust slurm options based on job requirements (slurm cheat sheet):

#!/bin/bash
#SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
#SBATCH -N 1   # Number of nodes
#SBATCH -n 1   # Number of tasks per node
#SBATCH -c 4   # Number of CPU cores per task
#SBATCH --mem=8G       # Memory required per node
#SBATCH --job-name=viennarna   # Job name
#SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
#SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
#SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
#SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

module purge   ### Optional, but highly recommended.
module load viennarna/XXXX     ### Latest version is recommended.