You can also try not to reinvent the wheel. Bio::SeqIO can parse genbank files. 
use Bio::SeqIO;
use strict;
my $in = Bio::SeqIO->new(-format =>'genbank',-file => $file);
# print the sequence from the genbank file
while( my $seq = $in->next_seq ) {
 print $seq->seq(), "\n";
}

[download]
Also see Ian Korf's lightweight GenBank parser: GBlite.pm

In reply to Re: Genbank file parsing by stajich
in thread Genbank file parsing by Anonymous Monk

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