The development of fast and inexpensive methods for sequencing bacterial genomes has led to a wealth of data, often with many genomes being sequenced of the same species or closely related organisms. Thus, there is a need for visualization methods that will allow easy comparison of many sequenced genomes to a defined reference strain. The BLASTatlas is one such tool that is useful for mapping and visualizing whole genome homology of genes and proteins within a reference strain compared to other strains or species of one or more prokaryotic organisms. We provide examples of BLASTatlases, including the Clostridium tetani plasmid p88, where homologues for toxin genes can be easily visualized in other sequenced Clostridium genomes, and for a Clostridium botulinum genome, compared to 14 other Clostridium genomes. DNA structural information is also included in the atlas to visualize the DNA chromosomal context of regions. Additional information can be added to these plots, and as an example we have added circles showing the probability of the DNA helix opening up under superhelical tension. The tool is SOAP compliant and WSDL (web services description language) files are located on our website: (http://www.cbs.dtu.dk/ws/BLASTatlas), where programming examples are available in Perl. By providing an interoperable method to carry out whole genome visualization of homology, this service offers bioinformaticians as well as biologists an easy-to-adopt workflow that can be directly called from the programming language of the user, hence enabling automation of repeated tasks. This tool can be relevant in many pangenomic as well as in metagenomic studies, by giving a quick overview of clusters of insertion sites, genomic islands and overall homology between a reference sequence and a data set.