Generic Synteny Browser: Example Data

These are instructions for setting up the example databases provided for GBrowse_syn in the GBrowse distribution.

Data Files

The oryza data source contains genome annotations in GFF3 flat files for two rice species and blastz-derived whole genome aligment data between the two species.

Configuration files

Configuration files for the two species can be found at the locations below. The oryza.synconf file is disabled pending installation of the joining database. rice_synteny.conf and wild_rice_synteny.conf are the configuration files for the individual species. They are already set up to use the in-memory adapter and the GFF3 flat files listed above.

Activate the Example Data Source

The joining database for the aligments currently only supports MySQL. To install the database:

1: create the database rice_synteny (you will need a MySQL account with CREATE and GRANT privileges). substitute your own user name and password for 'user' and 'pass'.

$ mysql -uuser -ppass 
mysql> create database rice_synteny;
Query OK, 1 row affected (0.00 sec)

mysql> grant SELECT on rice_synteny.* to 'www-data'@'localhost';
Query OK, 0 rows affected (0.02 sec)

mysql> quit
Bye
2: populate the database using the gbrowse_syn_load_alignments_msa.pl script (pre-installed with GBrowse). This will load the CLUSTALW-formated alignment file above into the database.
# we have to uncompress the alignment data
$ sudo gunzip $HTDOCS/databases/gbrowse_syn/alignments/rice.aln.gz
$ gbrowse_syn_load_alignments_msa.pl -u user -p pass -d rice_synteny -c $HTDOCS/databases/gbrowse_syn/alignments/rice.aln
3: active the oryza gbrwose_syn configuration file by renaming it (root-level acess required).
# as a sudoer
$ sudo mv $CONF/synteny/oryza.synconf.disabled $CONF/synteny/oryza.synconf

# or as root
% mv $CONF/synteny/oryza.synconf.disabled $CONF/synteny/oryza.synconf