[InterMine Dev] Storage of long sequences

Fengyuan Hu fh293 at cam.ac.uk
Tue Mar 12 17:10:54 GMT 2013


Hi JD,

If I'm correct, you need three tables:
sequencefeature
intermine_sequence
clob

foreign keys:
sequencefeature.sequenceid = intermine_sequence.id
intermine_sequence.residues = clob.clobid

the actually sequence string is in clob table.

Cheers
Fengyuan


On 11/03/13 20:56, JD Wong wrote:
> Hi Julie,
>
> intermine_sequence seems to map to residues, Alex mentioned sequences 
> are stored in CLOBs.  For debugging purposes, do you know where I can 
> find these?
>
> Thanks,
> -JD
>
> On Mon, Mar 11, 2013 at 3:18 PM, Julie Sullivan <julie at flymine.org 
> <mailto:julie at flymine.org>> wrote:
>
>     "sequence" is marked as a reserved word (mistakenly imo), so the
>     table is called "intermine_sequence".
>
>
>     On 11/03/13 18:41, JD Wong wrote:
>
>         Hello developer list,
>
>         In my mine's production database, I'm looking for a query to
>         display the
>         sequence for a specific protein.  Does anybody know where in
>         the database
>         sequences are stored?
>
>         Thank you!
>         -JD
>
>
>
>
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>
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