Tools for generating a list of known DNA binding motifs for a DNA binding protein

Question

[dk0319]

I have figured out how to extract fasta sequences from a bed file and then run motif discovery on it. Similarly, I have run my motif results in TOMTOM to identify proteins with similar motifs. But, I have yet to find a reliable way of searching for known DNA motifs by protein ID/name. What I want, ideally, is to input a TF protein name and get a list of known DNA motif associated with said TF. Any suggestions or recommendations on how to do this would be greatly appreciated. I figure MEMEsuite has a way but it is not outwardly clear. Cheers

[i.sudbery]

Sounds like you want FIMO (Find Individual Motif Occurrences) from the MEME?

[dk0319]

So that will give me the sequences containing a known DNA motif that I input. What I want, ideally, is to input a TF protein name and get a list of known DNA motif associated with said TF.

[i.sudbery]

Oh, I see. Right, in that case you need to be looking at one of the Motif databases. There are several. The best, unfortunately are commerical, and you need to pay for them.

The most commonly used free database is JASPAR (http://jaspar.genereg.net/)

Personally, if you are looking at humans or mice, I tend to use HOCOMOCO (https://hocomoco11.autosome.ru/). It has fewer motifs than JASPAR, but I tend to have a higher confidence in each one.

[dk0319]

This is what I was looking for. Thank you

Answer 1

[Alex Reynolds]

I have a few answers on Biostars and Bioinformatics Stack Exchange about using FIMO.

Here's a starter: A: TF binding site analysis - how to filter hits?

The idea is that you generate a whole-genome set of TF binding sites for your TF database of interest, and then you filter them as needed for your regions of interest, if needed.