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.

<<<<<<< HEAD
$ cd /var/www/gbrowse2/databases/gbrowse_syn/alignments
$ sudo gunzip rice.aln.gz
$ gbrowse_syn_load_alignments_msa.pl -u user -p pass -d rice_synteny -c -v rice.aln
=======
$ cd /var/lib/gbrowse2/databases/gbrowse_syn/alignments
$ gunzip -c rice.aln.gz | gbrowse_syn_load_alignments_msa.pl -u user -p pass -d rice_synteny -c -v -
>>>>>>> master
Where 'user' and 'pass' correspond to a mysql account with root-level privileges

3: activate the oryza gbrwose_syn configuration file by renaming it (root-level acess may be required).

<<<<<<< HEAD
# as a sudoer
$ sudo mv /etc/gbrowse2/synteny/oryza.synconf.disabled /etc/gbrowse2/synteny/oryza.synconf

# or as root
% mv /etc/gbrowse2/synteny/oryza.synconf.disabled /etc/gbrowse2/synteny/oryza.synconf
=======
$ mv /etc/gbrowse2/synteny/oryza.synconf.disabled /etc/gbrowse2/synteny/oryza.synconf
>>>>>>> master

Now reload this page and view the result!

Advanced (optional)

You can speed up the image loading time by putting your species' GFF3 data into relational MySQL databases. 1: create a database for each of the GFF

data files (rice.gff3 and wild_rice.gff3).

# create a mysql database for the rice data
$ mysql -uuser -ppass

mysql> create database rice;
Query OK, 1 row affected (0.00 sec)

mysql> grant SELECT on rice.* to 'www-data'@'localhost';
Query OK, 0 rows affected (0.00 sec)

mysql> create database wild_rice;
Query OK, 1 row affected (0.00 sec)

mysql> grant SELECT on wild_rice.* to 'www-data'@'localhost';
Query OK, 0 rows affected (0.00 sec)
2: populate the database using the bp_seqfeature_load.pl (pre-installed as part of BioPerl with GBrowse). This will load the <<<<<<< HEAD GFF3 data into a mySQL relational database. Note the mySQL user will need CREATE and INSERT privileges.
$ bp_seqfeature_load.pl -u user -p pass -d rice -c -f /var/www/gbrowse2/$GBROWSE_ROOT/databases/gbrowse_syn/rice/rice.gff3
loading /var/www/html/gbrowse/databases/gbrowse_syn/rice/rice.gff3...
Building object tree... 1.05s7s
Loading bulk data into database... 0.67s
load time: 31.40s

$ bp_seqfeature_load.pl -u user -p pass -d wild_rice -c -f /var/www/gbrowse2/$GBROWSE_ROOT/databases/gbrowse_syn/wild_rice/wild_rice.gff3
loading /var/www/html/gbrowse/databases/gbrowse_syn/wild_rice/wild_rice.gff3...
Building object tree... 1.15s9s
Loading bulk data into database... 0.69s
load time: 31.93s

3: Modify the following stanza in each configurations file (rice_syntency.conf and wild_rice_synteny), changing the dsn argumant as required for each data source. ======= GFF3 data into a MySQL relational database. >>>>>>> master Note the MySQL user will need CREATE and INSERT privileges.
<<<<<<< HEAD


Note the mySQL user will need CREATE and INSERT privileges.
$ bp_seqfeature_load.pl -u user -p pass -d rice -c -f /var/www/gbrowse2/$GBROWSE_ROOT/databases/gbrowse_syn/rice/rice.gff3
=======
$ bp_seqfeature_load.pl -u user -p pass -d rice -c -f /var/lib/gbrowse2/databases/gbrowse_syn/rice/rice.gff3
>>>>>>> master
loading /var/www/html/gbrowse/databases/gbrowse_syn/rice/rice.gff3...
Building object tree... 1.05s7s
Loading bulk data into database... 0.67s
load time: 31.40s

<<<<<<< HEAD
$ bp_seqfeature_load.pl -u user -p pass -d wild_rice -c -f /var/www/gbrowse2/$GBROWSE_ROOT/databases/gbrowse_syn/wild_rice/wild_rice.gff3
=======
$ bp_seqfeature_load.pl -u user -p pass -d wild_rice -c -f /var/lib/gbrowse2/databases/gbrowse_syn/wild_rice/wild_rice.gff3
>>>>>>> master
loading /var/www/html/gbrowse/databases/gbrowse_syn/wild_rice/wild_rice.gff3...
Building object tree... 1.15s9s
Loading bulk data into database... 0.69s
load time: 31.93s

3: Modify the following stanza in each configurations file (rice_syntency.conf and wild_rice_synteny), changing the dsn argumant as required for each data source.