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

[Nick Loman]

Hi Michael

You need a join on seqfeature_qualifier_value to get this detail. This 
table stores feature qualifiers as key/value pairs, with the 
corresponding key name ('name', 'product', etc.) belonging to the 
relation 'term', so you'll need to join on that too.

HTH

Cheers

Nick


Michael Muratet wrote:
> 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
>
>
>
>
>
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