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:[EMAIL PROTECTED] > Sent: 05 June 2003 10:17 > To: Y D Sun > Cc: [EMAIL PROTECTED] > 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. > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
