Welcome to the Monastery, BioUs2003. You'll note that while monks here try to be helpful, they do want well defined problems and will generally ask that you demonstrate that you've put work into solving the issue on your own. See How do I post a question effectively?.

In particular, note that because you did not wrap your code snippet in <code> tags, your regular expression classes got turned into links.

One challenge with your post is that the only well defined part of your problem is "How do I split after a K or R that is not followed by a P?" and that is that part that answered yourself. Of course, there's a typo in your suggested answer, and it should read

my @arr = split /(?<=[KR])(?=[^P])/;
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presuming you do not whichwish to perform the deprecated implicit split.

So, can you define in algorithmic terms what the following means?

The program should be able to read in FASTA-format protein sequences and return the individual peptides after digestion. Also, it should consider missed cleavages too.

Update: s/which/wish/ corrected as per below. It's been a long week.