An important step in unravelling the transcriptional regulatory network of an organism is to identify, for each transcription factor, all of its DNA binding sites. Several approaches are commonly used in searching for a transcription factors binding sites, including consensus sequences and position-specific scoring matrices. In addition, methods that compute the average number of nucleotide matches between a putative site and all known sites can be employed. Such basic approaches can all be naturally extended by incorporating pairwise nucleotide dependencies and per-position information content. In this paper, we evaluate the effectiveness of these basic approaches and their extensions in finding binding sites for a transcription factor of interest without erroneously identifying other genomic sequences.