I think this line: 
if ($protein =~ m/(KR)!P/g)

[download]
is looking for "KR"... NOT "K" or "R".

I think what you meant to do was: 
if ($protein =~ m/(K|R)!P/g)

[download]

In reply to Re: Bioinformatics: Regex loop, no output by james28909
in thread Bioinformatics: Regex loop, no output by TamaDP

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