This technique is used to determine precise thermodynamic parameters such as the binding affinity of proteins and DNA. The temperature of two identical cells containing a known concentration of TF is monitored. The ligand (DNA) with a putative site or not is added to the cells in precisely measured aliquots. The difference in temperature observed after adding the ligand, because in one cell it binds to the target while in the other it does not, can be used to compute the energetics of the reaction and therefore the binding affinity of the TF for the DNA fragment.

Once the binding motif for a TF is known, this motif (which essentially defines a pattern) can be used to scan sequences in order to search for putative TF-binding site. This is useful, for instance, when trying to identify TF-binding site in ChIP-chip data. Searching for TF-binding site can be done in numerous ways. The most basic method is consensus search, in sequences are scored according to how many mismatches they have with the consensus sequence for the motif. A more elaborate way of searching involves using regular expressions, which allow to search for more loosely defined motifs [e.g. C(C/G)AT]. Common algorithms for this type of search include Pattern Locator and the DNA Pattern Find method of the SMS2 suite, but also some word processors. Finally, the mainstream way of conducting TF-binding site search is through the use of position-specific scoring matrices, which basically count the occurrences of each base at each position of the motif and use the inferred frequencies to score candidate sites. Algorithms in this last category include TFSEARCH, FITOM, CONSITE, TESS and MatInspector.