If you are storing gene sequences in an XML-like markup, why not just use XML? Now you have the power of XML::Parser, XML::Twig, etc. at your disposal. You can also use DTD to enforce rules.

UPDATE:
Here is some code for you to play with, just install XML::Simple first. Notice how easy it is for me to get the individual attributes from the XML tag:

use strict;
use warnings;
use XML::Simple;

my $data = do {local $/;<DATA>};
my $xml  = XMLin($data);

print $xml->{label}, "\n";
print $xml->{id},    "\n";

__DATA__
<?xml version="1.0" ?>
<gene id = "3" label = "gene_of_interest" />
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jeffa

L-LL-L--L-LL-L--L-LL-L--
-R--R-RR-R--R-RR-R--R-RR
B--B--B--B--B--B--B--B--
H---H---H---H---H---H---
(the triplet paradiddle with high-hat)