The impact of phylogenetic footprinting analysis. Both (a-c) a high-quality set (14 genes and 40 verified sites), and (d-f) a larger collection of promoters (57 genes and 110 sites, from the TRANSFAC database [20, 21]) were analyzed. (a,d) Comparison of the selectivity (defined as the average number of predictions per 100 bp, using all models) between orthologous and single-sequence analysis modes. (b,e) Comparison of the sensitivity (the portion of 40 or 110 verified sites, respectively, that are detected with the given setting) between orthologous and single-sequence analysis modes. (c,f) Ratios of the number of sites detected in single-sequence mode to the number detected in orthologous-sequence mode; the pair: single-sequence ratios are displayed for both sensitivity (detected verified sites) and selectivity (all predicted sites).