Existing computational methods that identify transcription factor (TF) binding sites on a genes promoter are plagued by significant inaccuracies. Binding of a TF to a particular sequence is assessed by comparing its similarity score, obtained from the TFs known position weight matrix (PWM), to a threshold. If the similarity score is above the threshold, the sequence is considered a putative binding site. Determining this threshold is a central part of the problem, for which no satisfactory biologically based solution exists.