The arrays contain data similar to this:
@truncated_sequences = qw(JFADLKGJLFLGJGAFDJ DSJLJFLDJSLF...E.T.C);
@triamino_combo = qw(AAA AAB AAC AAD.......e.t.c);

foreach $prot_string (@truncated_sequences) {
	foreach $tri_seq (@triamino_combo) {
		while ($prot_string =~ /$tri_seq/g) {
			$tri_freq{$tri_seq}++;
			}
	}
}

##</code><code>##

foreach $prot_string (@truncated_sequences) {
	foreach $tri_seq (@triamino_combo) {
		if ($prot_string =~ /$tri_seq/g) {
			$tri_freq{$tri_seq}++;
			}
		else {
			$tri_freq{$tri_seq} = "0";
			}
	}
}