In conclusion, the SEED integration of genomic data now contains over 5,000 complete or nearly complete genomes, a constantly updated set of curated annotations embodied in a large and growing collection of encoded subsystems, and a derived set of protein families. The client-server code discussed in this article gives users easy programmatic access to the data in the SEED. It has already been successfully been used for building other applications, such as finding prophages in microbial genomes [43] , desktop-based RAST genome annotation and comparison (manuscript in preparation), and real-time annotation of metagenomes (RTMG, URL: http://edwards.sdsu.edu/rtmg [39] ). We encourage researchers to use this software to retrieve and analyze data from the SEED database and we believe that the underlying implementation of these new servers is efficient enough to address the needs of most users and we will continue providing occasional stand-alone versions of the SEED to users who need more performance or privacy.