use Bio::SeqIO; my $sequences = Bio::SeqIO->new( -file => "sequence.fasta", -format => "fasta", ); while ( my $dna = $sequences->next_seq ){ my $protein = $dna->translate( -codontable_id => 1, # standard genetic code -frame => 0, #reading-frame offset 0 ); print $dna->display_id, "\n"; print $protein->seq, "\n\n"; }