How to use rSNP_Tools?
rSNP_Tools is an active Java-script applet, for application of the weight matrices stored in the MATRIX database to recognition of the possible transcription factor (TF) binding to the regulatory site damaged/appeared due to mutations.
To recognize the TF-candidate, which binds to regulatory site damaged/appeared due to mutation, load the Java-applet rSNP_Tools and fulfill the following 3 steps.
Step 1 (by hand) Evaluate the transcription factor binding sites (TF-site) Recognition Scores by using MATRIX Tools (see Help). Input TF-site Scores values into boxes (cross-section of the site name and the appropriate DNA-chain). As the result, each TF-site is represented as the 2xN-dimensional numerical vector (here: N is the number of mutated variants). Authors recommend to characterize each of 41 TF listed.
Step 2 (by hand) Insert the experimental data on alteration of TF/DNA-binding (gel mobility shift assay, relative transcription activity, etc.).
Step 3 (automated) Click the option "Calculate". In the Section "Prediction", the predicted TF-candidates or the message about errors will appear. For denotations, see Step 2.