Hi monks,

I am here with a new query. Hope to get a quick reply.
I am try to search for the number of occurrence of 10 hexamer word in a big file of fasta sequence.
I want to get the number of occurrence of each hexamer at each position till 5000, which is the longest sequence.
the code i wrote is given below

#!/usr/bin/perl

use Data::Dumper;

open $f,$ARGV[0];

while(<$f>)
{
        chomp;
        $id = $_; #eat up the header line
        chomp($s = <$f>);
        if($s !~ /^>/)
        {
            push @seq,$s;    
        }
}

open $fa, "top_10_hexamers.txt";

while(<$fa>)
{
        chomp;
        $hx{$_}++; #hash of 10 hexamer
}

@words = sort keys %hx;

for($i = 1;$i < 5000;$i++)
{
        for($j = 0;$j <= $#words;$j++)
        {
                $result[$i][$j] = 0; # array of 5000 columns of positi
+on and words as columns 
        }
}

foreach $x(@seq)
{
                for($j = 0; $j < (length($x) - 6);$j++)
                {
                        $wrd = substr $x,$j,6;  #getting the hexamer c
+ombinations
                        foreach $w(@words)
                        {
                                if($w eq $wrd)  # comparing with the w
+ord
                                {
                                        $result->{$j}->{$wrd}++; # try
+ing to get position, word and frequency
                                }
                        }
                }
                $wrd = "";
}
print  Dumper $result;
[download]

It worked for me when my sequences where 50 bases long. I used to get a hash named $VAR1. But Now I am working with 5000, and it prints $VAR1 = undef;
Can any one help me with this problem.
Thank you in advance,

Best regards,
Deepak