Hi Thomas, I download the Embl files from
http://www.ebi.ac.uk/cgi-bin/genomes/genomes.cgi?genomes=Bacteria In the list, for example, No. 11 (BA000040) and 88 (BA000030) are large files. I find a problem in my PostgreSQL installation. I didn't build JDBC driver in it. Is this the cause of poor performance? I will reinstall it. However, BioSQL code does work without this build, slowly of course. George > -----Original Message----- > From: Thomas Down [mailto:[EMAIL PROTECTED] > Sent: 06 June 2003 14:33 > To: Y D Sun > Cc: [EMAIL PROTECTED] > Subject: Re: [Biojava-l] Different implementation of Sequence? > > > On Fri, Jun 06, 2003 at 10:33:28AM +0100, Y D Sun wrote: > > > > > -----Original Message----- > > > From: Thomas Down [mailto:[EMAIL PROTECTED] > > > Sent: 05 June 2003 22:58 > > > To: [EMAIL PROTECTED] > > > Cc: Y D Sun; Thomas Down; [EMAIL PROTECTED] > > > Subject: Re: [Biojava-l] Different implementation of Sequence? > > > > > > > > > Once upon a time, David Huen wrote: > > > > On Thursday 05 Jun 2003 6:07 pm, Y D Sun wrote: > > > > > Having created the indices as following and restarted > > > > > postmaster, > > > > > the performance of feature filtering is even worse. Maybe > > > MySQL is a > > > > > better choice than PostgreSQL. Does anyone have the similar > > > > > experience? > > > > > > > > > Was the access code exactly as you depicted it? ie. only > > > filtering on > > > > "CDS". > > > > Also what was the dataset you searched? was it the same > > > dataset in both > > > > EMBL flat file and BioSQL? What is your version of > > > postgresql and what was > > > > the platform? > > > > > > > > Yes, that is the exact code I use to filter CDS on one > sequence. The > > same code is used for the same sequence loaded from Embl file and > > PostgreSQL database. The execution times (for one sequence only) in > > two cases are highly diverse . > > > > I installed PostgreSQL 7.3.2 on Linux 2.4.20. > > > > The database contains 10 complete bacterial sequences with > length from > > 2M to 9M (Embl file size 9M to 18M). > > Hmmm... > > That amount of data definitely ought to be handled without > any big problems. On the other hand, it's enough that if > a lot of the database accesses we're going for indices, it > could plausibly take a minute or so. > > I've attached a new schema file which is compatible with the > one on the website, but has some extra CREATE INDEX > statements. Could you try again with that. If that doesn't > help, it might be worth trying MySQL to get a different datapoint. > > Finally, could you point me to one of the EMBL files you use > (preferably the biggest one), and I'll do some testing at some point. > > Thomas. > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
