It's supposed to be for an assignment and we must use REGEXPS...

That's akin to being asked to do a gainer off a diving board when just learning to swim. Especially so if you're in bioinformatics. From my experience, it would be more pedagogically sound to first learn to proficiently wield the (BioPerl) tools, then learn how to forge such tools...

If you must, however, use a regex in your script, perhaps the following will be helpful:

use strict;
use warnings;
use Bio::SeqIO;

my $filename = 'sequences.gen';

my $stream = Bio::SeqIO->new(
    -file   => $filename,
    -format => 'GenBank'
);

while ( my $seq = $stream->next_seq() ) {
    my $trans = $seq->translate();
    print $trans->seq(), "\n";
}

my $string = 'This script uses a regex.';
$string =~ s/uses/doesn't use/;
print $string;
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