Figure 2.

Screen shot of bicoid summary page within FlyFactorSurvey. (top) Header information for each factor contains identification information, the type(s) of DNA binding domains found within the gene and links to factor information in Flybase (36), Unipro (40) and FlyMine (33). (bottom) Recognition motifs determined for the factor through different methods, under different conditions or assayed via different sequencing methods are displayed in independent panels. Each panel displays the recognition motif as a Sequence logo (35) and download buttons to obtain count, position-specific probability (PSPM) or position-specific scoring (PSSM) matrices. The other information panel summarizes the methods used to select and sequence the factor binding sites. For motifs determined using the B1H system, the expression vector and the selection conditions are indicated where different stringencies can result in motifs with different complexity. In this example, only two of the four bicoid motif panels within the database are shown; these panels illustrate that the increased inhibitor concentration used in the selection to generate the lower panel resulted in a more stringent motif. For each individual motif, a direct link is provided to view the relative frequency of the motif in the Drosophila genome using Genome Surveyor (see Figure 3).