Does mySQL have UNION? If so you can do this: 
$sql = qq/  SELECT DISTINCT min(escore) as escore, org_id
            FROM blast, protein
            WHERE EXISTS (  SELECT id2, escore, org_id2
                            FROM blast, protein
                            WHERE id1 = id
                            AND text_id = ?
                            UNION
                            SELECT id1, escore, org_id1
                            FROM blast, protein
                            WHERE id2 = id
                            AND text_id = ? )
             GROUP BY org_id
          /;

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UNION in T-SQL gets rid of duplicate rows for you. So if UNION works the same way in mySQL then you reduce the overhead of making multiple queries and you won't need a temp table.

Update: Updated the query to include the DISTINCT and GROUP BY.

In reply to Re: speeding up mySQL query in .pm by monktim
in thread speeding up mySQL query in .pm by Anonymous Monk

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