> -----Original Message----- > From: Thomas Down [mailto:[EMAIL PROTECTED] > Sent: 10 June 2003 09:56 > To: Y D Sun > Cc: [EMAIL PROTECTED] > Subject: Re: [Biojava-l] Elapsed time of feature filtering > > > Once upon a time, Y D Sun wrote: > > I find that the elapsed time of filtering CDS for a sequence is > > proportional to the total number of sequences stored in a database. > > For exmaple, when there is only one sequence in the database, the > > filtering takes 5 seconds. If one more sequence is added to the DB, > > the filtering time for one sequence will take about 10 > seconds. When > > there are 3 sequences in DB, the filtering time will be about 15 > > seconds. > > Hi... > > I'm trying to reproduce this. I've started with a clean > database and loaded the schema I sent to you last week. I've > then inserted multiple copies of BA000040.embl (renamed each time, > obviously) and tried fetching CDS for one of the sequences. > With two copies loaded, this takes 6.3 seconds. With three > copies it does increase slightly, but only to 6.9 seconds. > Loading a fourth copy at the moment, but so far I'm not > really seeing the problem you're reporting. >
I would like to clarify one important point. Is biosqldb-pg.sql (you sent to me) the ONLY schema required to install in a database? Other two schemas, i.e., biosqldb-assembly-pg.sql and biosql-accelerators-pg.sql, are not required to install. I would also like to know the PostgreSQL version and OS you are using. How long it takes to add a sequence to the database in your case? For me, it takes 10 hours to insert a BA000040 sequence to DB. Thanks. George > (It would, of course, be nice if things went faster than 6 > seconds. On the other hand, I'm running this in a completely > untuned PostgreSQL installation on my laptop [256Mb memory, > slowish disk]. On a decent server with a RAID of modern > disks, the time would be negligable. And even just doing a > bit of basic postgres-tuning would help). > > Thomas. > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
