The SQL below makes sense. However it is extremely slow. Am I right in thinking that a join (MySQL) could be used and that the code could dispense with the embedded Perl?

    my $sql_count_A_Ref_vs_Comp = "

  SELECT '".$Reference."', '".$Comparitor."', A.entity_name FROM e_ann
+otation_090812.annotation A 
    WHERE A.user IN (
        SELECT T.Line FROM e_annotation_090812.Temp_table T
    )
    AND A.entity_name IN (
        SELECT B.entity_name from e_annotation_090812.annotation B 
            WHERE B.user IN (
                SELECT U.Line FROM  e_annotation_090812.Temp_table U
            )
            AND B.entity_name LIKE '_%' AND B.evidence_code NOT LIKE  
+'%_________8__' AND B.centre LIKE '".$Reference."'  
            )
    AND A.entity_name LIKE '_%' AND A.evidence_code NOT LIKE  '%______
+___8__' AND A.centre LIKE '".$Comparitor."'  

    ";
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