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

my $in  = Bio::SeqIO->new( -file => 'file1.fasta',  -format => 'Fasta' );
my $out = Bio::SeqIO->new( -file => '>file2.fasta', -format => 'Fasta' );

while ( my $seq = $in->next_seq() ) {
	my $newSeq = Bio::Seq->new(
		-display_id => $seq->id,
		-seq        => 'aaaa' . $seq->seq
	);
	$out->write_seq($newSeq);
}

##</code><code>##

>dddd
aaaaabcdef
>eeee
aaaabcdef

##</code><code>##

'aaaa' . $seq->seq