How to predict transcription factor binding site?

To predict transcription factor binding site in DNA, you may use the following tools:

PROMO is a virtual laboratory for the identification of putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. TFBS defined in the TRANSFAC database are used to construct specific binding site weight matrices for TFBS prediction. The user can inspect the result of the search through a graphical interface and downloadable text files.

JASPAR is the largest open-access database of curated and non-redundant transcription factor (TF) binding profiles from six different taxonomic groups.