The Annotation Support Server supports two distinct capabilities relating to the annotation of genomes: de novo annotation of protein or DNA sequences, and aggregation of annotations into subsystems. The Annotation Support Server accepts either DNA or protein sequence as input and, depending on the user options, can either use existing gene calls or invoke standard gene callers (e.g., GLIMMER-3 for protein-encoding genes). The server also houses newly developed high-performance methods to assign function to protein sequences or regions of genomic DNA sequences, based on FIGfams [22] . Below is an example application using these methods that produces a relatively accurate annotation of most microbial genomes within a few minutes. To evaluate the technology, users are encouraged to simply submit a known prokaryotic genome to the server for annotation.