The following program at http://servers.theseed.org/sapling/ server.cgi?code=server_paper_example4.pl illustrates the potential for constructing custom tools by going through all of the protein-encoding genes in all of the complete prokaryotic genomes maintained within the SEED looking for ''hypothetical proteins'' that tend to co-occur with genes encoding functions that can be connected to subsystems. The program constructs a table showing the following: This table can therefore be used to suggest functions for hypothetical proteins that could be tested experimentally. A copy of the code is provided (Supporting Information S1).