Modeling tag density profile and the detection of binding sites. (A) Shown is the tag density profile resulting from a single binding site. The binding site is at position 0. In this example, the average DNA fragment length is 120 bp, and the peak of this curve is at the position 49 bp from the assumed binding site. We use only part of the tag density curve (the right side of the red line) when detecting binding sites. (B) Shown is the schema of binding site detection. Given the modeled tag density profile, a least-squares fitting strategy is adopted to detect binding sites for both the forward and reverse strands. We take the goodness of fit as the criterion to identify binding sites, and the associated regression slope as the relative binding affinity. The two DNA strands are processed separately and the results from the both strand are then combined.