You're enabling warnings and strictures, and that's very good, but in the OPed code you have two variables that are undeclared (that I can see): @listes and $file (update: now fixed). This code will not compile, and it's very important to present compilable code to the monks lest they grow grumpy. Please see Short, Self-Contained, Correct Example.

That said, the word counting loop

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

jumps out at me. My thought was similar to fleet-fingered Athanasius's here (update: and almost-as-fleet-fingered Tux's here :), but rather than using split to exclude what is not wanted, I'd suggest defining a pattern $rx_word to extract anything that looks like a word that you might want to count. If the extracted word is in the pre-existing %count hash, count it. Something like (untested):

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;
    }
[download]

Obviously, the proper definition of $rx_word is critical! Only you can determine what this proper definition is. (If you define it right, you don't even need to bother chomp-ing anything.)

(I would have suggested the technique described in haukex's Building Regex Alternations Dynamically, but I suspect your word list is so big that it would capsize the regex compiler | see Update below. But you might try it anyway; it might be faster if it works at all.)

Update: I had thought that there was a hard limit to regex alternations that would cause compilation to fail, but it seems there is not — or if there is, it's much greater than 60K words! What I may have been thinking of is a limit to trie-optimization that causes a fallback to literal ordered alternation at some point. Given that that's the case, I would encourage you to try the dynamic alternation technique. I now expect it to work, and the only question is if it has a speed advantage.

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