#!/bin/bash
#SBATCH --job-name=viennarna-2.4.17-case
#SBATCH --partition=batch
#SBATCH --time=1:00:00
#SBATCH --nodes=1

module load gcc/9.2.0 viennarna/2.4.17

RNAfold -p < 5S.seq
$VIENNARNA_ROOT/share/ViennaRNA/bin/mountain.pl 5S_dp.ps
$VIENNARNA_ROOT/share/ViennaRNA/bin/relplot.pl 5S_ss.ps 5S_dp.ps > 5S_rss.ps
$VIENNARNA_ROOT/share/ViennaRNA/bin/rotate_ss.pl -a 180 -m 5S_rss.ps > 5S_rot.ps
RNAfold < 5S.seq > 5S.fold
RNAplot --pre "76 107 82 102 GREEN BFmark 44 49 0.8 0.8 0.8 Fomark \
     	1 15 8 RED omark 80 cmark 80 -0.23 -1.2 (pos80) Label 90 95 BLUE Fomark" < 5S.fold