Nucleic Acids Research, 2007, Vol. 35, No. 22 7587 Figure 7. EcoCyc genome browser showing display tracks. The promoter locations highlighted below each gene were predicted computationally (25) and can be download from the Web (see http://regulondb.ccg.unam.mx/data/PromoterPredictionSet.txt). Figure 8. The EcoCyc comparative genome browser centered at E. coli K-12 gene copA and its orthologs in Shigella ﬂexneri and E. coli EDL933. This comparative view shows that K-12 copA is an ortholog of genes with no assigned functions in the two other strains, despite their orthology and similar length to copA. The comparative view also shows how the orthologous region continues for many genes upstream in K-12 and Shigella, but ends at ybaT for K-12 and EDL933. DISCUSSION AND SUMMARY EcoCyc provides a rich and multidimensional annotation of the E. coli genome that is coupled with a large complement of software tools for querying and visualiza- tion of the EcoCyc data. EcoCyc contains a ‘living’ version of the E. coli annotation, subject to regular updates to gene sequences, functions and locations in response to advancing knowl- edge about this organism. We have recently performed the ﬁrst in a regular series of computational reannotations of the E. coli genome using the JCVI automated annotation pipeline, resulting in modiﬁcations to the annotations of 94 genes in EcoCyc. These and all other updates to the genome can be visualized using the EcoCyc genome browser, which can also be used to compare related genome regions across multiple organisms, and to overlay other information on the genome via the tracks feature. The dimensions of annotation within the current version (11.1) of EcoCyc are as follows. (i) The genome sequence is annotated with the positions of genes, promoters, terminators and transcription factor binding sites.