Background
The increasing number of published complete microbial genomes has revolutionized biological sciences and is driving a paradigm shift in microbiology. While this genomic revolution has made the reconstruction of an organism's metabolism from genomic data achievable, predicting the pathogenic potential of host-associated microbes is still in its early stages; hence, developing innovative bioinformatics tools that integrate microbiologists' expertise and experimental laboratory data with sequence data remains a necessity. For this purpose, the NIH-funded National Microbial Pathogen Data Resource (NMPDR, http://www.nmpdr.org) was established as a bioinformatics resource center for specific bacterial pathogens, including staphylococci, streptococci, and sexually transmitted bacteria [1]. Genomes in NMPDR are annotated by the recently developed subsystems annotation technology [2, 3], available from the SEED environment http://theseed.uchicago.edu/FIG/index.cgi. This technology relies on analyzing genes in their chromosomal context and combines the accuracy of human curation with the speed of automated propagation [2].