Well I see several problems with your script.

First your missing a / in your shebang statement.

When you declare the annotation array at the top of the script you have it mispelled. Your warnings should have pointed out to you that @annotation wasn't declared.

Your also passing your variables into your get_dna sub wrong. @_ is going to return the variables in the same order you passed them so the scalar value of @annotation is getting passed into $line and $file is getting passed into $seq. Atleast I think you didn;t mean to do that.

A better way to do this would be to just declare your @annotation array inside your get_dna sub and then if you need to access it outside of that sub again just return an array ref.

HTH.

-Prime