The bat has been implicated as a major reservoir for viruses of extreme pathogenicity in humans, and suffers substantially less disease when infected by these viruses than humans do. In addition, bat populations in North America are declining rapidly as a result of white-nose syndrome, an emergent disease associated with a fungal pathogen [35]. These facts, and others, suggest that the study of host defense and immunity in these unique creatures would benefit the pursuit of ecological and human health. The major obstacle in this undertaking is the lack of reagents that would make such investigations possible. One way to get this effort underway is to take advantage of the rich store of information contained in existing partial genome sequences. Although the information available in these genome databases requires more careful treatment for its extraction than is required for a complete, assembled genome, we have developed methods that facilitate this task, and have demonstrated their utility.