Let's see if I can still do this:

my $ar_data = $dbh->selectall_arrayref(qq (
SELECT noot.Reference, aap.Comparitor, aap.entity_name
FROM (
    SELECT ? AS Comparitor, entity_name
    FROM e_annotation_090812.annotation AS A
    JOIN e_annotation_090812.Temp_table AS T ON A.user = T.Line
    WHERE
        IFNULL(A.entity_name, '') <> ''
        AND A.evidence_code NOT LIKE '%_________8__'
        AND A.centre = ?
) AS aap
JOIN (
    SELECT ? AS Reference, entity_name
    FROM e_annotation_090812.annotation AS B
    JOIN e_annotation_090812.Temp_table AS U ON B.user = U.Line
    WHERE
        IFNULL(B.entity_name, '') <> ''
        AND B.evidence_code NOT LIKE '%_________8__'
        AND B.centre = ?
) AS noot ON aap.entity_name = noot.entity_name
), { Slice => {} }, ".${Comparitor}.", ".${Comparitor}.", ".${Referenc
+e}.", ".${Reference}.") or die("Error executing query: " . $dbh->errs
+tr);
[download]

Note that this is untested :)
Feedback is appreciated

Edit: Could you provide a small portion of (dummy) testdata to work with, as well as the DDL (the result of SHOW CREATE TABLE e_annotation_090812.annotation) of both tables?
This is handy to find further optimizations (for example, if evidence_code is a numerical field, using LIKE is very bad as it needs to typecast and thus can't use an index if present).

Edit2: Changed centre LIKE ? to centre = ? which should be better unless you're using wildcards (_ or %) in $Reference or $Comparitor

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