Good luck

This is what I was expecting. Is there any software you know of that can do this, i.e. you input a list, it automatically detects TFs, finds their "PSWM" matrices (or other), then automatically scans the remaining genes to look for TFBS (and perhaps ranks them, respectively for each TF)

Oh, and thanks a lot for the answer, of course :)

For what you desire I would suggest Motifviz's Possum. You can input your list using the JASPAR Core database (a database of PSWMs); the output is a series of stressed TFBSs for some TF in your sequences. This is a "quick and dirty" method, you could need something more complex and reliable, depending on your scopes.

For what concerns the detection of the TFs you should somehow use the annotation of your sequences, then make a script to retrieve only the desired TFs from the JASPAR database, generate a file containing the resulting list of PSWMs and input it. But it is not useful, I would simply input the whole database.

OK I see, so put in everything, then filter the output for the TFs that were in the original list?

Exactly, I would do so.

I wanted to do the same thing and some of the replies can be found here. Unfortunately, I haven't gotten around to doing it yet (waiting for data on more TFs)