I am try to search for the number of occurrence of 10 hexamer word in a big file of fasta sequence.
Did you try using BioPerl (http://bioperl.org)?
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
If you want to initialise your array for better handling of large data, look there: Re^3: how apply large memory with perl?
. By the way, this initialisation is lost because you initialize an array and work later with a hash reference. strict
would never allow it.
Sorry if my advice was wrong.