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c:\@Work\Perl\monks>perl -wMstrict -le
"my @proteins = qw(
...
Peptide is 'AAA'
Peptide is 'AAAK'
Peptide is 'AAA'

c:\@Work\Perl\monks>perl -wMstrict -le
"my @proteins = qw(
...
Peptide is 'AAA'
Peptide is 'AAAK'
Peptide is 'AAA'

my @peptides =           # 4. and the pieces are peptides.
  map  split($cleave),   # 3. split at each cleavage point...
  grep m{ $cleave }xms,  # 2. that can be cleaved, ...
  @proteins              # 1. for each protein...
  ;