Hello:
I was trying most of the day to turning up my GBrowse instance which was extremely slow and always time-out.
I found that for some reason, the two fields are not indexed by Gbrowse when creating the database tables:
table: feature
Fields: start,end
This caused significant slowness in my installation, where I have 54 millions rows in this table.
Indexing these 2 fields improved the speed for same query from 19.4 sec to 0.1 sec.
# original table schema:
CREATE TABLE `feature`
( `id` int(10) NOT NULL AUTO_INCREMENT, `typeid` int(10) NOT NULL,
`seqid` int(10) DEFAULT NULL,
`start` int(11) DEFAULT NULL,
`end` int(11) DEFAULT NULL,
`strand` tinyint(4) DEFAULT '0',
`tier` tinyint(4) DEFAULT NULL,
`bin` int(11) DEFAULT NULL,
`indexed` tinyint(4) DEFAULT '1',
`object` mediumblob NOT NULL,
PRIMARY KEY (`id`),
KEY `seqid` (`seqid`,`tier`,`bin`,`typeid`),
KEY `typeid` (`typeid`)
) ENGINE=MyISAM AUTO_INCREMENT=1371 DEFAULT CHARSET=latin1
If you faced same performance issue, you may want to check the index.
Lishuang Shen
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