If you don't need to keep the K or R items on which to cut the string, you could try this (demonstrated under the Perl debugger): 
  DB<6> $p = 'ALTAMCMNVWEITYHKGSDVNRRASFAQPPPQPPPPLLAIKPASDASD';

  DB<7> @b = split /[KR](?!P)/, $p;

  DB<8> x \@b;
0  ARRAY(0x6004f0f88)
   0  'ALTAMCMNVWEITYH'
   1  'GSDVN'
   2  ''
   3  'ASFAQPPPQPPPPLLAIKPASDASD'

[download]
If you need to keep those K and R items, then this might be easier: 
  DB<10> p $p
ALTAMCMNVWEITYHKGSDVNRRASFAQPPPQPPPPLLAIKPASDASD
  DB<11> $p = 'ALTAMCMNVWEITYHKGSDVNRRASFAQPPPQPPPPLLAIKPASDASD';

  DB<12> $p =~ s/([KR])(?!P)/$1=/g;

  DB<21> p $p
ALTAMCMNVWEITYHK=GSDVNR=R=ASFAQPPPQPPPPLLAIKPASDASD

[download]
In the latter case, you can then just split the resulting string on /=/.

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

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