Your code runs in O(@a * @b) time because of the grep nested inside the foreach. The hash approach will run in O(A + @b), where A is the time to build the hash %seen out of the values of @a (probably about @a*log(@a)). Hashes should be faster if the data sets are somewhat large.

If the two lists of DNs are sorted initially, you can use a merge algorithm (as in the unix comm program). That is an optimal solution, because it takes O(@a + @b) time, and there's no way to solve the problem without examining everything in both lists. If you have to sort the lists first, that's more expensive than the hash method.

Update: Now that I'm getting analysis of algorithms paged back in, I'm thinking A should have been @a in the first paragraph. The hashtable has to expand about log(@a) times, but each time it only has to reconsider the elements that were previously inserted, so it's @a + @a/2 + @a/4 + ... = @a*2, which is proportional to @a.