[Biojava-l] Different implementation of Sequence?

[Thomas Down]

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.