[Biojava-l] Different implementation of Sequence?

[Y D Sun]

> -----Original Message-----
> From: Thomas Down [mailto:thomas at derkholm.net] 
> Sent: 05 June 2003 22:58
> To: smh1008 at cus.cam.ac.uk
> Cc: Y D Sun; Thomas Down; biojava-l at biojava.org
> 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).  

George

> > I think we need some details to try to get to the bottom of 
> this one, 
> > the
> > more the better ;-)  In my experience, while postgresql may 
> not be faster, 
> > I've never known it to be this much worse.  Something is 
> wrong here and 
> > we'd like to fix it.
> 
> Yes, I'm definitely a bit worried.
> 
> From one of your earlier messages, it sounds like you only 
> have around 10 sequences loaded.  How big are these and how 
> many features? Frankly, unless your database is pretty large, 
> the queries shouldn't be taking as long as you say even 
> without any indices at all. Combined with the problems 
> creating indices, and VACUUM making matters worse rather than 
> better, I wonder if your postgres installation might be 
> feeling a bit sickly.
> 
> What postgres version are you using?
> 
>     Thomas.
>