Approaches to site analysis

Among the most popular methods to identify potential transcription factor binding sites (TFBSs) is the use of position-specific scoring or positional weight matrices (PSSM or PWM). The TRANSFAC® database, the gold standard in the field, harbors the largest collection of PWMs. They are used to predict TFBSs either by MATCH Suite, which is part of the TRANSFAC®2.0 online resource, or by a number of programs that are included in the geneXplain platform.