This: 
while (<>) {

[download]
is wrong, because you assigned a file handler to your input file. So, this should be: 
while (<$PROTFILE>) {

[download]
Otherwise, I am not sure why you want to set to paragraph mode.

There may be some other problems, but that should help you to get going.

In reply to Re^2: remove entries with duplicate characters by Laurent_R
in thread remove entries with duplicate characters by davi54

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
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