Using TF matrices to predict TF binding sites (TFBS) in regions of interest.

This is my plan:

**a. Download TF matrices**

I have seen TRANSFAC and JASPAR mentioned in relation to TF matrices. I have found some text files in the JASPAR database that seem like what I need and I will probably use these. Would anybody know if these are any different from the TRANSFAC matrices? Any other resources for matrices?

**b. Predict TFBS in sequence of interest**

For each TF matrix, predict where TFBS could be found in the sequences of interest. I have looked at the TFBS module for perl and although I don't want to doubt that what it does is right, the way that it searches for TFBS is not clear to me and so I wouldn't want to use it in a serious analysis.

My questions:

Are there any easy ways to bulk download TF matrices for all known TFs? (vertebrate, fly, nematode - separate for each species)

Is there a fast and usable TFBS prediction program?

- has to run from the command line
- has to be fast (I have quite a few sequences)

Since I am completely at a loss and TF prediction is not exactly my area of expertise, I don't know if what I'm asking for is irrelevant, solved 100 times already etc. Feel free to just point me to some relevant reviews or such and/or your favourite programs. It seems that all resources I get are from the early 00s and many are not still functional.

Great package! I had been looking for something like this for some time.

Nice to hear ... let me know if its useful.

This seems interesting, I'm not so good in python but maybe I could use it.

Hi i have a problem like you, i want to know if you could solved your problem with GIST. i don't know how can i run it. it hasnt any user guide. thanks a lot in advance

Is accurate enough to use TFBS matrices from humans to predict TFBS for other vertebrates ? Is there any relevant paper you can point me out? Is there also any up-to-date dabase with TFBS matrices? thanks a lot

Please check this paper and the related database CISBP: Weirauch, M. T., et al. (2014). "Determination and inference of eukaryotic transcription factor sequence specificity." Cell 158(6): 1431-1443.