[InterMine Dev] Storage of long sequences

JD Wong jdmswong at gmail.com
Tue Mar 12 19:32:35 GMT 2013


Hi Fengyuan,

That's what I'm looking for, thank you for your help!

-JD

On Tue, Mar 12, 2013 at 1:10 PM, Fengyuan Hu <fh293 at cam.ac.uk> wrote:

>  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> 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
>>>
>>>
>>>
>>>
>>>  _______________________________________________
>>> dev mailing list
>>> dev at intermine.org
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>
>>
>
>
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>
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