Chado query HOWTO: Protein/Transcript -> RefSeq ID

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Chado query HOWTO: Protein/Transcript -> RefSeq ID

Postby Josh Goodman » Tue Mar 24, 2009 9:58 am

This query returns a two column list that contains the FlyBase ID of the transcript or protein in the first column and the corresponding RefSeq ID in the second. Please note that this fetches data for all Drosophila species.

Code: Select all
select f.uniquename as fbid ,dbx.accession as refseq from feature f, feature_dbxref fdbx, dbxref dbx, db
         where f.is_obsolete=false and f.uniquename ~ '^FB(pp|tr)[0-9]+$' and
                   fdbx.is_current=true and upper(db.name)='REFSEQ' and
                   f.feature_id=fdbx.feature_id and fdbx.dbxref_id=dbx.dbxref_id and
                   dbx.db_id=db.db_id;
Josh Goodman
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