However I am unsure how to go about it. Should I used my genome as a blast db then blast the two known genomes against this?
If so do I then take the genes present and absent in both known genomes and blast them against each other?
One option would be to query the proteins of the 3 genomes against e.g. pfam (with hmmer) and then extract the number of shared features between the proteomes from that. Also, maybe they tell in the text or MM what they actually did there..