# Program commands

# Dataset :
# see all files in http://rssf.i2bc.paris-saclay.fr/suppl_data/Targetbench
# sRNA : coli_sRNA_v5.fa
# mRNA : NC_000913_CDS_-200nt_100nt.fa
# True targets (102 pairs): coli_targetpairs_V5.tsv 

# ============================================================================

# TargetRNA2 (online version at http://cs.wellesley.edu/~btjaden/TargetRNA2/advanced.html)

# Authors : Brian Tjaden (btjaden@wellesley.edu)
# (btjaden@wellesley.edu)

# Parameters :
# Replicon name : Escherichia coli str. K-12 substr. MG1655
# sRNA conservation and accessibiliy : on
# NTs upstream : 200
# NTs downstream : 100
# Hybridization seed : 7
# NTs in interaction region : 20
# mRNA structural accessibility : on
# P-value threshold : 1
# Filter size : 5000

# ============================================================================

# RNAplex (Version : 0.2)

# Authors : Tafer H, Hofacker IL
# [ivo@tbi.univie.ac.at]

# Accessibility computed with RNAplfold (V1.8)
RNAplfold -u 45 -O < coli_sRNA_v5.fa
RNAplfold -W 240 -L 160 -u 45 -O < NC_000913_CDS_-200nt_100nt.fa

# Command line : 
RNAplex -t NC_000913_CDS_-200nt_100nt.fa -q coli_sRNA_v5.fa -l 40 -z 20 -a ./access/ > results_targetRNA.txt

# ============================================================================

# IntaRNA (Version : IntaRNAa)

# Authors : Anke Busch, Andreas S. Richter, and Rolf Backofen
# [backofen@informatik.uni-freiburg.de]

# Command line :
IntaRNA -m coli_sRNA_v5.fa -t NC_000913_CDS_-200nt_100nt.fa -o -p 7 -s 0 > IntaRNA_results.txt

# ============================================================================

# CopraRNA V1.2.7 (online version at http://rna.informatik.uni-freiburg.de/CopraRNA/Input.jsp)

# Authors : Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Jörg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
# [jens.georg@biologie.uni-freiburg.de]  [backofen@informatik.uni-freiburg.de]

# sRNA alignments :
# - when possible we use precomputed results (ArcZ, ChiX, CyaR, DsrA, FnrS, GcvB, GlmZ, MicA, MicC, MicF, OmrA, OmrB, OxyS, RprA, RybB, RyhB, SgrS, Spot42 )
# - IstR : align_IstR.fa
# - RseX : align_RseX.fa
# - RydC : align_RydC.fa
# - McaS : not enough sequences found

# Other parameters :
# organism of interest : NC_000913 (Escherichia coli K 12 substr MG1655 uid57779)
# Extract sequences around: start codon
# nt up : 200
# nt down : 100

# ============================================================================

# In case one also wants to try Risearch:
# RIsearch (Version : 1.0)

# Authors : Wenzel A (wenzel@rth.dk), Akbasli E, Gorodkin J
# [gorodkin@rth.dk]

# Command line :  RIsearch -q coli_sRNA_v5.fa -t NC_000913_CDS_-200nt_100nt.fa -d 30 > Risearch_results.txt