/***********************************************************
  RIsearch v 1.2   --   RNA-RNA, RNA-DNA, DNA-DNA interaction search

  Copyright 2012 Anne Wenzel <wenzel@rth.dk> (RIsearch v.1.0 and v.1.1)
  Copyright 2021 Giulia I Corsi <giulia@rth.dk> (Extension of RIsearch v.1.1 in RIsearch v.1.2)

  This file is part of RIsearch.

  RIsearch 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.

  RIsearch 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 RIsearch, see file COPYING.
  If not, see <http://www.gnu.org/licenses/>.

***********************************************************/



=== HOWTO: compile & run ===

$ make RISEARCH
$ ./RIsearch -q query.fa -t target.fa

query and target may contain several sequences, RIsearch will scan all vs. all
Alternatively single sequences can be given directly on commandline with
-Q acgu -T acgu

See the Manual included in the RIsearch folder for a complete list of options and usage examples.

=== Citation ===

If you find this software useful for your research, please cite the following work:

Anne Wenzel, Erdinç Akbaşlı, and Jan Gorodkin.
RIsearch: fast RNA–RNA interaction search using a simplified nearest-neighbor energy model.
Bioinformatics (2012) 28(21): 2738–2746. 

=== Contact ===

wenzel@rth.dk


