Hi Perlmonks,

I am a beginner in perl programming. I have two strings of unequal sizes (15 & 12 letters) i.e. $a="AGAGATATTCAAATT"; and $b="TCGAACGTCGAG"; In comparing the two given strings $a and $b, I am interested to count the types of changes (A to T i.e. A2T, G2A, A2G etc.) for 1st, 2nd and 3rd positions of all 3-letter words between two strings. Use of hash and dumper together appears very complicated to me. I donot know which perl code I should use in such counting. Since the two strings are small, one can do it manually. I wish if perl code could do the same task then it can be used in comparing two strings as long as 100 letters (which is difficult to do manually). May I expect to get help from Perlmonks in counting the types of changes between two strings?

#!/usr/bin/perl-w
use strict;
use Data::Dump qw[ pp ];
my $a="AGAGATATTCAAATT";
my $b="TCGAACGTCGAG";
my (%first,%second,%third);
my @trilet1 = $a =~ /.../g;
my @trilet2 = $b =~ /.../g;
use Data::Dump qw[ pp ];
Code?????

for my $p ( 0 .. length( $seq1 ) - 1 ) {
    my $c1 = substr $seq1, $p, 1;
    my $c2 = substr $seq2, $p, 1;
    next if $c1 eq $c2;
    ++$subs{ $c1 . '2' . $c2 };
}
pp \%first,%second, %third;
exit;

<p>The result should look like:</p>

<code>Counting Results:
{ For 1st position of all 3-letter words:
A2T=> 1,
G2A=> 1,
A2G=> 1,
C2G=> 1,

For 2nd position of all 3-letter words:
G2C=> 1,

For 3rd position of all 3-letter words:
A2G=> 2,
T2C=> 2,
}

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In reply to How can I count the types of changes in 1st, 2nd and 3rd positions of all 3-letter words in comparing two separate strings of unequal length? by supriyoch_2008

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