Figure 3

A customizable graphical representation of DNA binding sites. The Scalable Vector Graphics visualization displays the genomic context of putative and known motifs in the upstream sequences of the operons. The user interface allows users to interact with the visualization. A) Hide de novo motifs. B) Hide known motifs from literature. C). Hide upstream regions without any putative or known motifs. D). Use standard coloring of putative motifs. E). Use coloring of putative motifs based on best hit with known motif. F). Every found motif can be displayed or hidden from the visualization using checkboxes. G) Known motifs can be displayed or hidden from the visualization using checkboxes. H). The scaling slider adjusts the width between the upstream sequences. I). The zooming slider allows for zooming of the visualization. J). The first structural gene of each operon is a large polygon, whilst the other genes are represented using smaller polygons. K). Genes coding for a putative regulator are colored red. Hovering with the mouse over the genes creates a tooltip displaying the function of the gene. L). Open polygons represent known binding sites derived from literature sources. M). Filled polygons depict putative motifs.