| | Re: Transcription factors binding site searching-why both strands?
The only reason not to search both strands would be if the directionality of binding had an effect on the transcription factor activity; i.e. the presence of the protein at the promoter is not sufficient for activity, but it has to present a specific surface to the transcription start site for some reason.
I think in most cases, the simple presence of a transcription factor is sufficient for it to do whatever it's trying to do, so it's important to search both strands for theoretical binding sites.
That said, most DNA binding elements are palindromic, so I'm not sure why reading one direction would give you more hits than reading in the other direction.