Major Sometimes we would make some manually modifications on a sequence or alignment. For example, I would write a fasta DNA sequence like:
>one_test_sequence
AAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTTTgtatttttttttttttttttttagGGGGGGGGGCCCCCCCCCCCCC
The lowercase region "gtatttttttttttttttttttag" means it is an intron region. However, when I load it into UGENE, all residues become uppercase and I can't recognize the intron region easily. Some other softwares such as BioEdit would keep the original base(uppercase or lowercase or mixed) in the sequence view.
I think it is not difficult to make this subtle change, right?
