
# 5sRNA
~/src/Mysrc/R-scape/bin/R-scape --outdir 6o9j_A/R-scape    --cacofold 6o9j_A/6o9j_A.sto        > 6o9j_A/6o9j_A.rscape
~/src/Mysrc/R-scape/bin/R-scape --outdir 6o9j_A/R-scape -s --cacofold 6o9j_A/RF00001_1_116.sto > 6o9j_A/RF00001_1_116.rscape 
~/src/Mysrc/R-scape/bin/R-scape --outdir 6o9j_A/R-scape -s --cacofold 6o9j_A/RF00001.seed.sto  > 6o9j_A/RF00001.seed.rscape

# Purine Riboswitch Aptamer
~/src/Mysrc/R-scape/bin/R-scape --outdir 2xnw_A/R-scape    --cacofold 2xnw_A/2xnw_A.sto        > 2xnw_A/2xnw_A.rscape
~/src/Mysrc/R-scape/bin/R-scape --outdir 2xnw_A/R-scape -s --cacofold 2xnw_A/RF00167_0_66.sto  > 2xnw_A/RF00167_0_66.rscape 
~/src/Mysrc/R-scape/bin/R-scape --outdir 2xnw_A/R-scape -s --cacofold 2xnw_A/RF00167.seed.sto  > 2xnw_A/RF00167.seed.rscape

# Glutamine Riboswitch Aptamer
~/src/Mysrc/R-scape/bin/R-scape --outdir 5ddp_A/R-scape    --cacofold 5ddp_A/5ddp_A.sto        > 5ddp_A/5ddp_A.rscape
~/src/Mysrc/R-scape/bin/R-scape --outdir 5ddp_A/R-scape -s --cacofold 5ddp_A/RF01739_0_60.sto  > 5ddp_A/RF01739_0_60.rscape 
~/src/Mysrc/R-scape/bin/R-scape --outdir 5ddp_A/R-scape -s --cacofold 5ddp_A/RF01739.seed.sto  > 5ddp_A/RF01739.seed.rscape

# Hammerhead_3 Ribozyme
~/src/Mysrc/R-scape/bin/R-scape --outdir 2qus_A/R-scape    --cacofold 2qus_A/2qus_A.sto        > 2qus_A/2qus_A.rscape
~/src/Mysrc/R-scape/bin/R-scape --outdir 2qus_A/R-scape -s --cacofold 2qus_A/RF00008_4_59.sto  > 2qus_A/RF00008_4_59.rscape 
~/src/Mysrc/R-scape/bin/R-scape --outdir 2qus_A/R-scape -s --cacofold 2qus_A/RF00008.seed.sto  > 2qus_A/RF00008.seed.rscape

# RNaseP Nuclear
~/src/Mysrc/R-scape/bin/R-scape --outdir 6ahr_A/R-scape    --cacofold 6ahr_A/6ahr_A.sto        > 6ahr_A/6ahr_A.rscape
~/src/Mysrc/R-scape/bin/R-scape --outdir 6ahr_A/R-scape -s --cacofold 6ahr_A/RF00009_4_336.sto > 6ahr_A/RF00009_4_336.rscape 
~/src/Mysrc/R-scape/bin/R-scape --outdir 6ahr_A/R-scape -s --cacofold 6ahr_A/RF00009.seed.sto  > 6ahr_A/RF00009.seed.rscape

~/src/Mysrc/R-scape/lib/hmmer/easel/miniapps/esl-alistat --list 6ahr_A/RF00009.seed.names 6ahr_A/RF00009.seed.sto
~/src/Mysrc/R-scape/lib/hmmer/easel/miniapps/esl-alimanip --seq-r 6ahr_A/RF00009.seed.names 6ahr_A/RF00009_4_336.sto > 6ahr_A/RF00009_4_336.full.v0.sto
~/src/Mysrc/R-scape/lib/hmmer/easel/miniapps/esl-alimanip --seq-k 6ahr_A/RF00009.seed.names 6ahr_A/RF00009_4_336.sto > 6ahr_A/RF00009_4_336.seed.v0.sto

~/src/Mysrc/R-scape/lib/hmmer/easel/miniapps/esl-reformat --mingap stockholm 6ahr_A/RF00009_4_336.seed.v0.sto > 6ahr_A/RF00009_4_336.seed.sto
~/src/Mysrc/R-scape/lib/hmmer/easel/miniapps/esl-reformat --mingap stockholm 6ahr_A/RF00009_4_336.full.v0.sto > 6ahr_A/RF00009_4_336.full.sto

~/src/Mysrc/R-scape/bin/R-scape --outdir 6ahr_A/R-scape -s --cacofold 6ahr_A/RF00009_4_336.seed.sto  > 6ahr_A/RF00009_4_336.seed.rscape
~/src/Mysrc/R-scape/bin/R-scape --outdir 6ahr_A/R-scape -s --cacofold 6ahr_A/RF00009_4_336.full.sto  > 6ahr_A/RF00009_4_336.full.rscape

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Figure 2
---------

# (a) 5S rRNA
6o9j_A/R-scape/6o9j_A_1.cacofold.R2R.sto.pdf 
# (b) 5S rRNA
6o9j_A/R-scape/RF00001_1_116_1.cacofold.R2R.sto.pdf
# (c) 5S rRNA 
6o9j_A/R-scape/RF00001_5S_rRNA.cacofold.R2R.sto.pdf

# (a) Purine
2xnw_A/R-scape/2xnw_A_1.cacofold.R2R.sto.pdf
# (b) Purine
2xnw_A/R-scape/RF00167_0_66_1.cacofold.R2R.sto.pdf
# (c) Purine
2xnw_A/R-scape/RF00167_Purine.cacofold.R2R.sto.pdf


Figure 2A
----------

# (a) Glutamine Riboswitch Aptamer
5ddp_A/R-scape/5ddp_A_1.cacofold.R2R.sto.pdf 
# (b) Glutamine Riboswitch Aptamer 
5ddp_A/R-scape/RF01739_0_60_1.cacofold.R2R.sto.pdf
# (c) Glutamine Riboswitch Aptamer 
5ddp_A/R-scape/RF01739_Glutamine.cacofold.R2R.sto.pdf


# (a) Hammerhead_3 Ribozyme
2qus_A/R-scape/2qus_A_1.cacofold.R2R.sto.pdf 
# (b) Hammerhead_3 Ribozyme
2qus_A/R-scape/RF00008_4_59_1.cacofold.R2R.sto.pdf
# (c) Hammerhead_3 Ribozyme 

# (a) RNaseP Nuclear
6ahr_A/R-scape/6ahr_A_1.cacofold.R2R.sto.pdf
# (b) RNaseP Nuclear
open 6ahr_A/R-scape/RF00009_4_336_1.R2R.sto.pdf
# (c) RNaseP Nuclear
6ahr_A/R-scape/RF00009_RNaseP_nuc.R2R.sto.pdf



