GBrowse_syn is a GBrowse-based synteny browser designed to display multiple genomes, with a central reference species compared to two or more additional species. It is included with the standard GBrowse package (version 1.69 and later).
GBrowse_syn is part of the GBrowse 2.0 package and was pre-installed when you went through the GBrowse 2.0 installation.
Update: We will need to update the GBrowse source to include features and bug patches not included in the CPAN distribution:
First, update Bio::Graphics
$ sudo cpan -i Bio::Graphics
Then check out a fresh copy of the current GBrowse 2 source code via subversion (svn).
$ cd /home/gmod/Downloads/sources $ svn co https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/trunk Generic-Genome-Browser $ cd Generic-Genome-Browser $ sudo perl Build.PL $ sudo ./Build install
NOTE: use the default options when prompted.
Now point your browser to http://localhost/cgi-bin/gb2/gbrowse_syn
The focus of the section of the course is on dealing with alignment or synteny data and using GBrowse_syn. However, how to generate whole genome alignments, identify orthologous regions, etc, are the subject of considerable interest, so some background reading is listed below:
There is detailed documentation on the GMOD wiki for how to install, configure and use GBrowse_syn. To get started, browse these pages: