How can we view and compare information on 1000’s of genomes

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? We have tools to visualise a single genome, how can we view and compare information on 1000’s of genomes? 

Description: the data consists of single and multiple genome sequences associated with annotations of genes, transcripts, proteins and other functional elements. This information is matched by evolutionary relationships between these elements from the genomes of different species.

Challenge: how can we annotate and visualise 100’s or even 1000’s of genomes? For example, to ask evolutionary questions about what is shared by these genomes.