If I understood your question clearly, here is my solution. You can use negative look behind regex and split function to accomplsh it. TIMTOWTDI.
$string = 'APADPKGSTIDRPDAARTLTVHKCEQTDTRGVKEGTRNEDPQAECKPVSDVEFTITKLN
+VD';
@arr = split /(?<!P)(K|R)/, $string;
print @arr;
output:
-------
APADPKGSTIDRPDAARTLTVHKCEQTDTRGVKEGTRNEDPQAECKPVSDVEFTITKLNVD
Take a look at perlre and split function.
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