[InterMine Dev] Storage of long sequences

Alex Kalderimis alex at intermine.org
Mon Mar 11 18:55:39 GMT 2013


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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