Hey, Thanks.I modified the code above as below to iterate over each value in the %seq hash and it works pretty fast :)

while (my $string = <IN1>) {
        chomp $string;
        #my ($value) = values %seq;
        foreach $value (values %seq) {
        my $result = () = $value =~ /$string/g;
         print "$string => $result\n";
        }
}
[download]