How to extract PRDM9 binding motifs in bed format?

Question

[reza.jabal]

I am seeking advice on relevant solution/database for extracting all PRDM9 motifs across human genome. Ideally I'd like the coordinates of start position and end position for such motifs across all human chromosomes.

Answer 1

[Alex Reynolds]

You might look for a PRDM9 motif model matrix from one of these TF databases: http://floresta.eead.csic.es/footprintdb/?databases

Once you have the model's matrix in MEME format, you could run that through FIMO to find putative binding sites (in BED format): http://meme-suite.org/doc/fimo.html

[reza.jabal]

Alex thanks a lot for your suggestion. It is super helpful!

Answer 2

[aays]

EMBOSS fuzznuc might solve your issue. The output isn't exactly in bed format, but it does return start/end coordinates in a table-formatted file and also allows for fuzzy searching, which is probably handy considering the degeneracy of the PRDM9 binding motif. (Caveat being that I haven't used it myself, however)

Edit: apologies, I realize your question is also asking about a database from which these motifs could be pulled. If I'm understanding that correctly, would the fasta sequence of the human reference genome work?

[reza.jabal]

Thanks a lot for your suggestion. Seems like a handy package that helps solving the problem!

Answer 3

[AB]

Not entirely sure if this will help but maybe you can try using the HOMER software's scanMotifGenomeWide.pl

[reza.jabal]

Thank you for your suggestion, I am looking for a database that such motifs could be pulled from in bed format?