The new phylogenetic footprinting reference collection of TFBSs allows for quantitative assessment of the performance of new methods. This is the largest collection of its kind available for
instance, the amount of flanking sequence used for mapping the locations of the sites onto genome sequences was lower in the previous study. These short fragments were mapped onto a commercial human genome assembly and the mapped regions compared to shotgun-generated fragments of mouse genomes from multiple strains. The alignment procedures were also different, with the older set aligned by BLAST [30] and assessed