... the part that I think is causing the error ...

Yes, indeed! It's just as ikegami first said 'way back in Re: trouble assigning values to hash! The trouble starts with the statement
    my ( $line, %seqs, $sequence, $date, $orig, $desg, $body );
in which a bunch of variables are defined and given no values. The 'Use of uninitialized value...' fireworks happen in the very next statement, which attempts to use all the uninitialized values (well, the scalars at any rate).

Have a nice weekend. We look forward to your first post on this topic Monday morning. :)
BTW: Your posted regexes still don't make any sense, but that's a discussion for Monday.