If * is in the original sequence no need to switch ---

ProtoGene.pl

@@ -1274,6 +1274,9 @@ sub buildCDSseq{
     my $locus  = 0;
     for(my $z=0; $z<=length($input_seq); $z++){
         if ( $z==length($input_seq) ){
+            if ( $input_seq =~ /\*$/ ){ # If * is in the original sequence no need to switch ---
+                $cdsSeq =~ s{\-\-\-$}{};
+            }
             $locus++;
             if ( exists($POSITIONS{$locus}) && ($POSITIONS{$locus} eq 'TAA' || $POSITIONS{$locus} eq 'TAG' || $POSITIONS{$locus} eq 'TGA') ){
                 $cdsSeq .= $POSITIONS{$locus};
@@ -1437,7 +1440,7 @@ sub revtransBuilding{
             $final_seq = $final_seq.reverse_trad($aa);
         }
         $readyname           =~ s{_G_$NTstatus _S_ $BLASTstatus }{_G_revtrans };
-        my $CDSreformatedSeq = $final_seq."---\n"; #FIXME: For stop codon ???
+        my $CDSreformatedSeq = $final_seq."---\n"; #FIXME For stop codon ???
         $CDSreformatedSeq    =~ s{([^\n]{60})}{$1\n}g;
         chomp $CDSreformatedSeq if ( $CDSreformatedSeq =~ /\n+$/ );
         print CDS "$readyname\n$CDSreformatedSeq";