Often researchers want to assess functionality of a TF binding site by ablating the site, or assess the role on affinity by optimizing or reducing the affinity of the site. It is important to ensure that the chosen mutation does not have any unintended sidefects. For example, a mutation that ablates your site of interest could also create a binding site that didn’t exist in the original sequence.

The Perturb Site Without Side Effects Module enumerates all mutations that either ablate, optimize affinity or reduce affinity the site. For each mutation, it reports any secondary effects on other TF binding sites the mutation has. The best mutation is one that has the intended effect (ablation or optimization) with minimal side effects.

This module can also be used to ensure PAM deletions for CRISPR experiments do not alter existing binding sites.