[Biojava-l] Elapsed time of feature filtering

[Y D Sun]

> -----Original Message-----
> From: Thomas Down [mailto:thomas at derkholm.net] 
> Sent: 10 June 2003 09:56
> To: Y D Sun
> Cc: biojava-l at biojava.org
> 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.
>