[Biojava-l] Different implementation of Sequence?

[Y D Sun]

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?

George

> -----Original Message-----
> From: Thomas Down [mailto:thomas at derkholm.net] 
> Sent: 05 June 2003 10:17
> To: Y D Sun
> Cc: biojava-l at biojava.org
> Subject: Re: [Biojava-l] Different implementation of Sequence?
> 
> 
> Once upon a time, Y D Sun wrote:
> >
> > > That said, the time you quote is very, very, slow.  Where did you 
> > > get the BioSQL schema from?  Some versions are circulating which 
> > > seem to be missing some critical "CREATE INDEX" statements, which 
> > > makes feature-filtering substantially slower than it should be...
> > 
> > I download the schema from 
> http://www.biojava.org/download/biosql/ and 
> > run them in 
> postgresql. Is there newer version?
> 
> Okay, the postgres version of that schema is missing many 
> "create index" commands (it was autogenerated from the MySQL 
> schema.  MySQL implicitly creates an index for the primary 
> key of a table, while PostgreSQL does not).
> 
> The most important one is:
> 
>     CREATE INDEX sf_pk ON seqfeature (seqfeature_id);
> 
> That should get the system running substantially faster.
> 
> Also try:
> 
>      CREATE INDEX ot_pk ON ontology_term (ontology_term_id);
>      CREATE INDEX sfs_pk ON seqfeature_source (seqfeature_source_id);
> 
> I'll try and get a better schema file up today.
> 
>     Thomas.
>