while (my $line = <$fh>) {
    chomp $line;
    foreach my $mot (keys (%count)) {
    chomp $mot;        
    foreach my $str ($line =~ /$mot/g) {
        $count{$str}++;
    }
    }    
}

##</code><code>##

my $rx_word = qr{ \b [[:alpha:]]+ \b }xms;  # a very naïve word!

while (my $line = <$fh>) {
    exists $count{$_} and ++$count{$_} for $line =~ m{ $rx_word }xmsg;
    }