Re: how do i count the 22 selected di-peptides from a multifasta file separately for each sequence

[hdb]

Why bother searching for specific pairs of letters? Just count them all, there are not so many of them, and then pick the counts you are interested in:

use strict;
use warnings;

my $line= 'AAALVDENEC';
my %counts;
$counts{substr $line, $_, 2}++ for 0..length($line)-2;

my @wanted = qw(AA AL DA DE DV VD DW QD SD HD ED DY VE EN EI KE NV VP 
+FV SS WK KK);
for (@wanted) {
  print "$_ => $counts{$_}\n" if defined $counts{$_};
}