<p>As title.</p>

<p>Because SELEX experiment can detect strong binding site of TF, and ChIP-seq experiment can detect both strong and weak binding site (due to the cross-linked).</p>

<p>So I wonder if PWM derived from SELEX still have the strong binding site property and PWM derived from ChIP-seq still have the strong and weak binding site property.</p>

<p>Or,it will lose the property when these two experiments model to PWM.</p>

<p>Any suggestion or papers will help.</p>

<p>Thanks</p>

The TFBSs by ChIP-seq data are usually divided into different groups (strong and weak, sometimes with an intermediate group: moderate) based on their binding strength. A common assumption is that "ChIP-seq signal values are correlated with the affinity of the TF-DNA binding" [ [*][1] ]

PWM alone helps us model the sequences at TFBSs but no such information about binding affinity, unless binding scores are also annotated.

 [1]: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003214