Figure 3

Demonstration of two different methods for obtaining the sequence n bases surrounding the known regulatory binding site. In the figure 'cr' refers to completely realistic generation where we find the closest downstream CDS location in the genome and extract n bases upstream from that CDS. 'sr' refers to extracting n/2 bases upstream and downstream of the center of the binding site. We assume that programs reverse complement sequences appropriately as needed by the method as part of the discovery procedure but provide upstream sequences on the positive strand relative to the downstream CDS. The known motif 'blackfile' sequence is represented by a black line over the binding site k that refers to the region that is bound by the transcription factor. The red regions in the diagram illustrate the actual binding positions known for motif k for those nucleotides that interact with the regulatory protein.