The user first must have a target sequence and mutated variants of interest for the (+) and (-) strands. For example, to use rSNP_Guide for analysis of the human platelet glycoprotein Ibb gene, GpIbb , promoter allele of which (“-133C/G”) has been associated with Bernard-Soulier syndrome, four DNA sequences should be initially prepared, such as: the wild-type allele “WT” (+)-chain, 5’-tgtgctatCtgccgctg-3’, and (-)-chain, 5’-cagcggcaGatagcaca-3'; and, the mutant allele “-133C/G”, 5’-tgtgctatGtgccgctg-3’ and 5’-cagcggcaCatagcaca-3' (where nucleotide alterations are colored and underlined).

In the upper section of the user interface window, a TF is selected. When a TF is clicked on, a window appears for its corresponding site recognition. The user enters into the input box each sequence variant and for each the button “Execute” is clicked. Clicking brings up a screen with the graphical representation of the TF site recognition score. With a single dominant peak, the corresponding score on the left axis is entered in the proper box in the user interface. In our example, the DNA sequence, “5’-tgtgctatGtgccgctg-3’”, “-133C/G” allele, (+)-chain, was entered into the AP-1 binding site recognition program. For this sequence variant, the AP-1 site recognition Score profile has a single peak with the maximal value “0”, which is put into the proper box. In the case of multiple peaks, the user can choose a peak according to relative height or proximity to a sequence region most likely to influence binding. When all sequence variants of interest have been examined and the data entered in the user interface, the next TF is selected and the process repeated.