The results of a genome-wide scanning simply using a short and degenerate sequence (as that represented by the PWM integrating the data for the Estrogen response element), will be riddled with false positives. Having said that,  a quick and dirty way to do what you want, is use RSAT (http://www.rsat.eu/). You can also use FIMO from the MEME Suite (http://meme-suite.org/tools/fimo). There are many other tools. A google search with "genome scanning pwm" will show many others.

You can find the PWM for the TF of your interest, here (http://cisbp.ccbr.utoronto.ca/).

Good luck!

-A

There are several ones. This web may help you:

https://abc.med.cornell.edu › t-promoter

In my hands Genomatix works very well, although it is not free. You can test it with a trial license.

The results of a genome-wide scanning simply using a short and degenerate sequence (as that represented by the PWM integrating the data for the Estrogen response element), will be riddled with false positives. Having said that,  a quick and dirty way to do what you want, is use RSAT (http://www.rsat.eu/). You can also use FIMO from the MEME Suite (http://meme-suite.org/tools/fimo). There are many other tools. A google search with "genome scanning pwm" will show many others.

You can find the PWM for the TF of your interest, here (http://cisbp.ccbr.utoronto.ca/).

Good luck!

-A

I have already used genomatix (matinspector) software trail version for promoter-transcription factor binding and it worked fine.