How to handle this will depend on both the character encoding of your input file and the character encoding of your output (in this case, the terminal). Once you know these you can use Encode to decode from your input and encode to your output.

Now, here are a few supplementary questions for you:

• Why no strict?
• Why do your comments refer throughout to protein sequences when instead you are dealing with a Swedish dictionary?
• Why persist with bareword filehandles? This combined with the lack of strict means that you did not spot that you have opened FILE but attempted to close PROTEINFILE.

If you can correct these and properly decode from and encode to the correct character encodings you should be all set. Good luck.