Freezer:

A join might be helpful, as you're guessing. Considering that it's using the same conditionals and tables, it would likely be good to refactor the SQL a bit. On first glance, it looks like you're using extremely similar conditions, so you could perhaps change it to:

SELECT '".$Reference."', '".$Comparitor."', A.entity_name 
FROM e_annotation_090812.annotation A 
join e_annotation_090812.Temp_table T on T.Line=A.user
where A.entity_name like '_%'
  and A.evidence_code not like '%_________8__'
  and (A.centre like '".$Reference."' or A.centre like '".$Comparitor.
+"')
[download]

I don't use mysql, but if it's like Oracle, then the "_" is a wildcard character, so effectively the first like expression is merely checking that the string is at least one character long, and the second checks that the string is at least 12 characters long with an 8 as the third-from-last character. The final like clauses could easily be converted to simple comparisons. So you could possibly gain a bit of speed (be sure to benchmark it!) by just doing the explicit checks:

SELECT '".$Reference."', '".$Comparitor."', A.entity_name 
FROM e_annotation_090812.annotation A 
join e_annotation_090812.Temp_table T on T.Line=A.user
where length(A.entity_name)>0
  and (
     length(A.evidence_code)<12 
     or substring(A.evidence_code,length(A.evidence_code)-2,1)<>'8')
  )
  and (A.centre = '".$Reference."' or A.centre = '".$Comparitor."')
[download]

Finally, to get rid of the trivial amount of embedded perl, you could use placeholders:

my $ST = $DB->prepare(<<EOSQL);
SELECT ?, ?, A.entity_name 
FROM e_annotation_090812.annotation A 
join e_annotation_090812.Temp_table T on T.Line=A.user
where length(A.entity_name)>0
  and (
     length(A.evidence_code)<12 
     or substring(A.evidence_code,length(A.evidence_code)-2,1)<>'8')
  )
  and (A.centre=? or A.centre=?)
EOSQL
$ST->execute($Reference, $Comparitor, ".$Reference.", ".$Comparitor.")
+;
[download]

Update: Changed != to <> and substr to substring Re^4: s/Perl/SQL/ ? as described by Anonymous Monk. I didn't *fully* fix substring, as I've never seen nor tried the form "substring(A.foo from 1 for 2)". I don't doubt that it's correct (I even double-checked the SQL92 and SQL2002 docs referenced at http://savage.net.au/SQL/.) It's just too ugly for me to consider. ;^)

...roboticus

When your only tool is a hammer, all problems look like your thumb.

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