Seems to work fine for me. I'm not sure exactly what you want to match with it, but this:

$string = <DATA>;

$right = quotemeta('</a>');
($temp, $id)= $string =~ m/(Gallus\sgallus|Chicken).*?([0-9]+)>.*?$rig
+ht.*?\n/i;

print "$temp: $id\n";

__DATA__
<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db
+=Nucleotide&list_uids=18656900&dopt=GenBank" >gb|AF468789.1|</a>  Gal
+lus gallus LIM domain-containing transcri...   <a href = #18656900> 4
+8</a>   0.006
[download]

prints this:

Gallus gallus: 18656900
[download]

-sauoq
"My two cents aren't worth a dime.";