The ERGO™ Genome Analysis System provides an in silico systems biology platform for the comprehensive analysis of organisms for which genomic DNA sequence data is available. ERGO™ is a third-generation bioinformatics suite offered exclusively by Integrated Genomics and represents the development of a multi-dimensional genome informatics platform supporting both automatic and manual genome-wide curation. Rather than merely repackaging known information, ERGO™ integrates genomic information with biochemical data, literature, and high-throughput analysis into a comprehensive user-friendly network of metabolic and non-metabolic pathways. ERGO™ users can take into account sequence similarity, protein and gene context clustering, occurrence profiles, regulatory and expression data, as well as functional hierarchies in order to obtain the best possible set of gene functional predictions. Using the ERGO™ system, a major part of the metabolism of an organism, can be reconstructed entirely in silico.