@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]

Your current algorithm would be more efficient as: 

@string = <IN1>;
chomp @string;

while ( my $string = <IN1> ) {
    chomp $string;
    my ( $value ) = values %seq;
    my $result = () = $value =~ /$string/ig;

     print "$string => $result\n";
     }

[download]

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

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