[BioSQL-l] Getting gene name, function etc. from biosql

[Michael Muratet]

Greetings

I am working on assembling gene CDS sequences on a medium scale, e.g.,  
for all S. aureus strains, and I'm trying to find a way to get gene  
names from biosql entries I created from Genbank files with  
load_seqdatabase.pl. I'm using a query like this:

SELECT
     c.seqfeature_id, b.strand, SUBSTR(a.seq, b.start_pos, b.end_pos- 
b.start_pos+1) as seq
FROM
     biosequence a
     JOIN
     seqfeature c
     ON (a.bioentry_id=c.bioentry_id)
     JOIN
     location b
     ON (b.seqfeature_id=c.seqfeature_id)
WHERE
     c.type_term_id=12
     AND
     c.bioentry_id=221

This seems to work OK to get the sequence with the provision that one  
needs to reverse complement the sequence if the strand is minus.

But I don't see anything in the schema that will allow me to identify  
the gene name or product from the seqfeature_id.

Is gene name or product in the schema somewhere and I've missed it?

Thanks

Mike


Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806