Overview: with the current advances in sequencing technologies and computer science the number of fully sequenced genomes of complex organisms, such as plants, mammals and birds, is likely to exceed 10,000 or more very soon. The availability of multiple genomes provides a number of challenges, such as, gene annotation and the description of the transcribed and the regulatory parts of each genome. Currently this can take months for a single genome, how can this be scaled up to 1000’s?