Reporter assay using the beta-galactosidase (lacZ) gene. The lacZ gene is typically fused to the promoter of interest. Differential regulation of the promoter mediated by the TF is assessed by induction of the system and evaluation of lacZ expression. Bacteria expressing lacZ appear blue when grown on a X-gal medium. The assay is often performed using a plasmid borne construction on a lacZ(def) strain.

As with motif discovery, TF-binding sites search benefits from a comparative genomics approach. Searching a single genome for TFBS will yield very noisy results. If a number of related genomes are searched, then the search results can be compared and strengthened by requiring that a site be located, for instance, in the promoter region of the same gene for at least two or three species. As in the case of motif discovery, these methods are not often applied to verify experimental results, but can be used to guide experimental research. For instance, comparative genomics searches can be implemented to detect good candidate sites, which are then verified using an experimental technique.