We have previously developed a general method based on the statistical technique of discriminant analysis to distinguish functional sites on nucleic acid sequences. The attributes used for discrimination include the accuracy of consensus sequence patterns measured by the perceptron algorithm, the base composition and periodicity, the free energy of snRNA and mRNA base pairing, the thermal stability map, and the Calladine-Dickerson rules for helical twist angle, roll angle, torsion angle and propeller twist angle. We discuss the usefulness and the further applicability of this method.