I just finished a chapter for a book, Methods in Avian Embryology, being edited by my boss, Marianne Bronner-Fraser. This chapter is intended for developmental biologists who are interested in locating regulatory modules and analyzing them for binding sites. It ended up being my outlet for a compilation of problems and drawbacks to computational search, and so it might be useful to non-biologists, too. I'd be happy to pass a copy on to people who are interested; drop me a line.

--titus