Which experiments generate Position Frequency Matrix?

Question

[Anisur Rahman]

From the JASPAR database, I can download Position Frequency Matrix (PFM) for transcription factors. My question is, how can we get such PFM for a transcription factor? Is there any experimental method or technique like ChIP-seq to generate PFM?

Answer 1

[ATpoint]

Yes, ChIP-seq or similar methods that assay the DNA binding of a protein. But for a reliable matrix you don't need one or two but many datasets. That is why curated repositories such as JASPAR or (my favorit) HOCOMOCO are valuable, as they base their PFMs on many datasets for the same protein.

[Anisur Rahman]

That was very helpful. Thank you for your reply.