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.
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.