There is an alternative to matching with overlapping patterns: 

#!/usr/bin/perl

# http://perlmonks.org/?node_id=1124725

use strict;

my @dipeptides = split /\|/,
  'AA|AL|DA|DE|DV|VD|DW|QD|SD|HD|ED|DY|VE|EN|EI|KE|NV|VP|FV|SS|WK|KK';

for my $line ( 'AAALVDENEC', 'AATLVDEGDG' )
  {
  my $sum = grep $line =~ $_, @dipeptides;
  my $abs = @dipeptides - $sum;
  print "$line sum: $sum  abs: $abs\n";
  }

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In reply to Re^3: how do i count the 22 selected di-peptides from a multifasta file separately for each sequence by Anonymous Monk
in thread how do i count the 22 selected di-peptides from a multifasta file separately for each sequence by SOMEN

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