PFM for CTCF in mm9 extremely difficult to find- or does one exist?

Apologies for the naive question but I am new to the field of Position Frequency matrices (PFMs). I am trying to find a PFM for CTCF binding in the mm9 version of the mouse genome...

I have searched JASPAR, TRANSFAC and http://ccg.vital-it.ch/pwmtools/pwmbrowse.html. None of the databases in these websites return a verifiable PFM for CTCF in the mm9 genome.

I also tried the R-packages TFBSTools, JASPAR2014 and JASPAR2016.

opts <- list(name="CTCF", species = "10090")
pfm <- getMatrixSet(JASPAR2014, opts)

And this returns 0 results.....

Does anyone know where I can get a PFM for CTCF in mm9?

assembly

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updated 8.9 years ago by jared.andrews07

• written 8.9 years ago by chrisclarkson100

1 answer

HOCOMOCO has it. I don't know if it's created by datasets from mm9, but I expect it probably is, and that shouldn't matter much for whatever you're doing with it anyway.

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written 8.9 years ago by jared.andrews07