note aitap <p><i><blockquote>I am try to search for the number of occurrence of 10 hexamer word in a big file of fasta sequence.</blockquote></i> Did you try using [mod://BioPerl] ([http://bioperl.org])?</p> <p><blockquote><c>for($i = 1;$i < 5000;$i++) { for($j = 0;$j <= $#words;$j++) { $result[$i][$j] = 0; # array of 5000 columns of position and words as columns } }</c></blockquote> If you want to initialise your array for better handling of large data, look there: [id://986487]. By the way, this initialisation is lost because you initialize an array and work later with a hash reference. [doc://strict] would never allow it.</p> <!-- Node text goes above. Div tags should contain sig only --> <div class="pmsig"><div class="pmsig-980564"> Sorry if my advice was wrong. </div></div> 1005742 1005742