[InterMine Dev] Storage of long sequences

JD Wong jdmswong at gmail.com
Mon Mar 11 19:13:13 GMT 2013


Hi Alex,

Sounds good, thanks for the fast reply!

-JD

On Mon, Mar 11, 2013 at 2:55 PM, Alex Kalderimis <alex at intermine.org> wrote:

> On Monday 11 March 2013 14:41:57 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
>
> For efficiency's sake, sequence is stored as a CLOB, and the sequence for a
> specific item is read out by index (or at least it is for nucleic sequence
> - I
> believe it is much the same for protein sequence).
>
> As for writing db queries, while that is possible intermine is meant to be
> a
> black-box of sorts and one isn't meant to rely on data being in certain
> tables, and you certainly aren't expected to write your own sql. May I
> suggest
> using the webservices for this? Of if you are in java-land, you can
> connect to
> the db using the object store itself, and perform ObjectStore queries
> natively.
>
> Alex
>
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