How do I search a promoter DNA sequence for potential transcription factor binding sites?
To search a DNA sequence for potential transcription factor binding sites, you can use one of the following tools/programs, which are supplied with TRANSFAC ® professional, MATCH TM or PATCH TM . PATCH TM compares the sequence with the site entries in TRANSFAC ® , MATCH TM compares it with the nucleotide distribution matrices. As a result you get a list of those sites or matrices, respectively, that matched your sequence. In addition to the tabular view, you can view your results graphically.