The DOE JGI is the global leader in generating genome sequences of plants, fungi, microbes, and metagenomes. As such, the genome sequence data processing and integration activities of its Science Programs have a “production” nature, in which tools developed based on computational biology methods are applied on data sets within the context of program-specific informatics systems. The institute’s comparative analysis systems have matured over the past years and are recognized as important resources for conducting genome and metagenome studies, empowering scientists around the world to conduct studies that otherwise would be very expensive or out of reach. They allow the users to analyze and improve the functional characterization of a vast number of publicly available genomes and metagenomes.