Question: How to extract PRDM9 binding motifs in bed format?
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gravatar for reza.jabal
2.3 years ago by
reza.jabal370
New York, USA
reza.jabal370 wrote:

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.

chip-seq genome • 864 views
ADD COMMENTlink modified 2.3 years ago by Alex Reynolds30k • written 2.3 years ago by reza.jabal370
2
gravatar for Alex Reynolds
2.3 years ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

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

ADD COMMENTlink written 2.3 years ago by Alex Reynolds30k

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

ADD REPLYlink written 2.3 years ago by reza.jabal370
1
gravatar for aays
2.3 years ago by
aays140
Canada
aays140 wrote:

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?

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by aays140

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

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by reza.jabal370
0
gravatar for Apoorva
2.3 years ago by
Apoorva250
United States
Apoorva250 wrote:

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

ADD COMMENTlink written 2.3 years ago by Apoorva250

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

ADD REPLYlink written 2.3 years ago by reza.jabal370
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