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 *.* to 'www-data'@'localhost'; Query OK, 0 rows affected (0.02 sec) mysql> quit Bye2: 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.
$ zcat /var/lib/gbrowse/databases/gbrowse_syn/alignments/rice.aln.gz | gbrowse_syn_load_alignments_msa.pl -u user -p pass -d rice_synteny -v -c -3: activate the oryza gbrwose_syn configuration file by renaming it (root-level acess required).
# as a sudoer $ sudo mv /etc/gbrowse/synteny/oryza.synconf.disabled /etc/gbrowse/synteny/oryza.synconf # or as root % mv /etc/gbrowse/synteny/oryza.synconf.disabled /etc/gbrowse/synteny/oryza.synconf
# create a mysql database for the rice data $ mysql -uuser -ppass mysql> create database rice; Query OK, 1 row affected (0.00 sec) mysql> create database wild_rice; Query OK, 1 row 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 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/html/gbrowse/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/html/gbrowse/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: 31.93s3: 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. You will need to set the permissions so you can edit the files
$ sudo chmod 644 /etc/gbrowse/synteny/*Change:
# from db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor memory -dir /var/lib/gbrowse/databases/gbrowse_syn/rice # to db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor DBI::mysql -dsn dbi:mysql:rice -user www-data
An example over sugarcane and sorghum genome synteny: