join will happily slurp up your list. You need a loop of some kind. How's this?

foreach (grep $_->[0] eq 'EMBL') {
    print OUT "DR EMBL;$_->[0];$_->[1];-.\n";
}
[download]

Sorry, no map in there, but I don't think you need it. :)

Update: Juerd caught a typo. Fixed!