**200**wrote:

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.

**20**• written 9.0 years ago by Panagiotis Alexiou •

**200**