Difference between unaligned and aligned FASTA file

[brucezepplin]

Hi everyone - this is probably a very simple question for most of you. What is the difference between the two. EMBL says that aligned has gaps to optimize alignment to a reference sequence. The - or . can refer to an insertion deletion, however I have some .faa files which contain both i.e.

AYW---TGHGGG...--QZX

Am I to assume - means a deletion and . means an extention?

And how do these gaps come about? I understand the need to optimize a seed sequence against a reference sequence, but which reference sequence is used?

Thanks for you help, and being patient with a basic question.

[maubp]

Which alignment tool are you talking about? Consult its documentation.