1) maybe Text::Levenshtein will help you here; it calculates the Levenshtein_distance for you,

Which is nothing like what he wants, since it allows indels. He wants hamming distance, so T::L would do the wrong thing.

efficiency is hard to define;

No it isn't: he probably wants to match many short strings against a long one (like a chromosome, with millions of characters) as quickly as possible.