GMorse 2.0

G-Mo.R-Se is a method aimed at using RNA-Seq short 
reads to build de novo gene models. First, candidate 
exons are built directly from the positions of the 
reads mapped on the genome (without any ab initio 
assembly of the reads), and all the possible splice 
junctions between those exons are tested against 
unmapped reads : the testing of junctions is directed 
by the information available in the RNA-Seq dataset 
rather than a priori knowledge about the genome. 
Exons can thus be chained into stranded gene models.

G-Mo.R-Se is distributed open-source under CeCILL 
FREE SOFTWARE LICENSE. Check out http://www.cecill.info/
for more information about the contents of this license.

G-Mo.R-Se's home on the web is http://www.genoscope.cns.fr/gmorse


PRE-REQUISITES
--------------

  - A Linux based operating system.
  - Binaries are provided for the following platform : Linux x86_64
  - Perl 5.8.0 or higher installed.
  - Perl graph library (http://search.cpan.org/~jhi/Graph-0.84/)
  - Perl GetOpt module (http://search.cpan.org/dist/Getopt-Long/)


DEPENDENCIES
------------
The two following binaries : fastarevcomp and fastatranslate
come from the exonerate software availaible under the LGPL
license. See http://www.ebi.ac.uk/~guy/exonerate/ for details.
The dbfstextract binary file uses the following shared library 
libbigloo_s-2.8c.so and libbigloogc-2.8c.so available under the 
LGPL license. See http://www-sop.inria.fr/mimosa/fp/Bigloo/ for 
details. 


INSTALLATION
------------

  1. Download the current tarball archive from http://www.genoscope.cns.fr/gmorse/download
     $$ wget http://www.genoscope.cns.fr/externe/gmorse/download/gmorse_latest.tar.gz
  2. Untar/unzip the archive
     $$ tar -zxvf gmorse_latest.tar.gz
     $$ cd gmorse
  3. Modify the GMORSE_DIR environment variable
     $$ export GMORSE_DIR=`pwd`
  4. Modify if needed the Perl and sh interpreters that have been set to 
     /usr/bin/perl and /bin/sh



RUNNING GMORSE
--------------

See README.txt file


ACKNOWLEDGMENTS
---------------
France Denoeud, Jean-Marc Aury - G-Mo.R-Se's authors

This work was financially supported by the Genoscope, 
Institut de Genomique, CEA and Agence Nationale de la 
Recherche (ANR).