Hi all, I have been working on getting the count of 16384 patterns in a large string(sequence) .However the code is very slow.Is there an efficient way to do this. I have researched on this a bit, but could not find any way.Below is my code : 

@string = <IN1>;
chomp @string;

foreach my $string (@string) {
     foreach $key (keys %seq) {
        chomp $string;
         study $seq{$key};
       my @matches = ($seq{$key} =~ /$string/ig);
        #print "@matches\n";
        $result{$string} = scalar(@matches);
        }

foreach my $s (keys %result) {
        print "$s => $result{$s}\n";
        }

[download]

Any help would be appreciated.Thanks

In reply to counting the number of 16384 pattern matches in a large DNA sequence by anonym

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