
============= siRNA off-target Dicovery Pipeline v1.0 ==============
====================================================================
 Pipeline package is composed of two executable Python scripts, 
 a user manual and a dummy data to be used in example runs 
 as explained in the user manual.

!!! PLEASE READ THE USER MANUAL before running any off-target !!!
!!!  predictions with this pipeline.                          !!!

========================== Prerequisites ===========================
 Both scripts use only main Python libraries that comes with Python
 itself, however, you need to have RIsearch2 and RNAplfold packages
 already installed and running in your system to be able to execute
 these scripts. 

 In case you are using an older Python version than 2.7, we provide 
 the "argparse" python package together with the code. 

============================== Scripts =============================
 ./src/pipeline.py : siRNA off-target Discovery Pipeline.

 ./src/run_RNAplfold_and_pack_results.py : Script that divides the 
    input target sequence in 100kb pieces, runs RNAplfold with them
    and packs the results into a binary format to be able to pass 
    them into the pipeline.

 Both scripts are executable.
============================= Citation =============================
 If you find this software useful for your research, 
 please cite the following work:

 RIsearch2: suffix array-based large-scale prediction of RNA-RNA 
  interactions and siRNA off-targets, Alkan F, Wenzel A, Palasca O, 
  Kerpedjiev P, Rudebeck AF, Stadler PF, Hofacker IL, Gorodkin J, 
  Nucleic Acids Res., 2017,  doi: 10.1093/nar/gkw1325 

============================== Contact =============================
ferro@rth.dk
gorodkin@rth.dk

============================ Licensing ============================
    --- siRNA off-target Discovery Pipeline v1.0 --- 
  siRNA off-targeting potential and off-targets prediction tool

  Copyright 2016 Ferhat Alkan <ferro@rth.dk>

  This file is part of siRNA off-target Discovery Pipeline.

  siRNA off-target Discovery Pipeline is free software: you can 
  redistribute it and/or modify it under the terms of the 
  GNU General Public License as published by the 
  Free Software Foundation, either version 3 of the License, or
  (at your option) any later version.

  siRNA off-target Discovery Pipeline is distributed in the hope
  that it will be useful, but WITHOUT ANY WARRANTY; without even 
  the implied warranty of MERCHANTABILITY or 
  FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with siRNA off-target Discovery Pipeline, see file COPYING.
  If not, see <http://www.gnu.org/licenses/>.
====================================================================
