NET-Seq
PB-Seq
PB–seq is a DNA-binding assay that allows the DNA-protein binding energy landscape to be characterized genome-wide, in the absence of chromatin. It belongs to the family of methods more commonly known as systematic evolution of ligands by exponential enrichment (SELEX). Genomic DNA is sonicated, size-selected, and purified. After hybridization to the DNA-binding protein the protein-bound DNA is isolated, extracted, and prepared for sequencing.
Pros:
- Determines binding efficiencies independent of chromatin structure
Cons:
- Not yet adopted widely by the scientific community