When creating a Bio::Seq object, always specify '-alphabet'.

modules/Bio/EnsEMBL/Exon.pm

@@ -1260,10 +1260,11 @@ sub peptide {
     $pep_str = $tr->translate->subseq($start, $end);
   }
 
-  return Bio::Seq->new(-seq => $pep_str, 
-		       -moltype => 'protein',
-		       -alphabet => 'protein',
-                       -id => $self->display_id);
+  return
+    Bio::Seq->new( -seq      => $pep_str,
+                   -moltype  => 'protein',
+                   -alphabet => 'protein',
+                   -id       => $self->display_id );
 }
 
 
@@ -1309,9 +1310,11 @@ sub seq {
     $self->{'_seq_cache'} = $seq;
   }
 
-  return Bio::Seq->new(-seq     => $self->{'_seq_cache'},
-                       -id      => $self->display_id,
-                       -moltype => 'dna');
+  return
+    Bio::Seq->new( -seq      => $self->{'_seq_cache'},
+                   -id       => $self->display_id,
+                   -moltype  => 'dna',
+                   -alphabet => 'dna' );
 }
 
 

modules/Bio/EnsEMBL/PredictionTranscript.pm

@@ -277,9 +277,10 @@ sub translation {
     $Xseq = "N"x$start_phase . $Xseq;
   }
 
-  my $tmpSeq = new Bio::Seq( -id => $self->display_id,
-			     -seq => $Xseq,
-			     -moltype => "dna" );
+  my $tmpSeq = new Bio::Seq( -id       => $self->display_id,
+                             -seq      => $Xseq,
+                             -moltype  => 'dna',
+                             -alphabet => 'dna' );
 
   return Bio::EnsEMBL::Translation->new
     (-ADAPTOR    => $pta,
@@ -335,7 +336,10 @@ sub translate {
   # if you want to have a terminal stop codon either comment this line out
   # or call translatable seq directly and produce a translation from it
 
-  my $bioseq = new Bio::Seq(  -id => $self->display_id, -seq => $dna, -moltype => 'dna' );
+  my $bioseq = new Bio::Seq( -id       => $self->display_id,
+                             -seq      => $dna,
+                             -moltype  => 'dna',
+                             -alphabet => 'dna' );
 
   my $translation = $bioseq->translate(undef,undef,undef,$codon_table_id);
 

modules/Bio/EnsEMBL/Transcript.pm

@@ -1405,10 +1405,11 @@ sub five_prime_utr {
 
   return undef if(!$seq);
 
-  return Bio::Seq->new(
-	       -DISPLAY_ID => $self->display_id,
-	       -MOLTYPE    => 'dna',
-	       -SEQ        => $seq);
+  return
+    Bio::Seq->new( -id       => $self->display_id,
+                   -moltype  => 'dna',
+                   -alphabet => 'dna',
+                   -seq      => $seq );
 }
 
 
@@ -1439,10 +1440,11 @@ sub three_prime_utr {
 
   return undef if(!$seq);
 
-  return Bio::Seq->new(
-	       -DISPLAY_ID => $self->display_id,
-	       -MOLTYPE    => 'dna',
-	       -SEQ        => $seq);
+  return
+    Bio::Seq->new( -id       => $self->display_id,
+                   -moltype  => 'dna',
+                   -alphabet => 'dna',
+                   -seq      => $seq );
 }
 
 
@@ -1626,11 +1628,13 @@ sub translate {
 =cut
 
 sub seq {
-  my( $self ) = @_;
-  return Bio::Seq->new
-    (-DISPLAY_ID => $self->display_id,
-     -MOLTYPE    => 'dna',
-     -SEQ        => $self->spliced_seq);
+  my ($self) = @_;
+
+  return
+    Bio::Seq->new( -id       => $self->display_id,
+                   -moltype  => 'dna',
+                   -alphabet => 'dna',
+                   -seq      => $self->spliced_seq );
 }