Here, we first report a novel method in which the “desired cross-spectrum” of the peptides Prp106—126, MSI-78A, and oxaldie 1 with the same biological activities is obtained by the multiplication of two cross-spectra derived from the RNA sequence and from the cognate amino acid sequence by discrete Fourier transform (DFT), respectively. Based on a well-known method reported previously, we investigated the cross-spectrum by the multiplication of two of three desired cross-spectra. As a result, we found that one prominent peak occurring in the three cross-spectra showed the same frequency when a binary scale was used as a parameter of nucleotide or amino acid in the analysis. Moreover, we examined the relationship between a binary scale and other physicochemical ones. Almost the same results could be reproduced when the absolute elctronegativity scale (or the absolute hardness one) was used, but not in the case of the hydrophobic or electron–ion interacting potential scale reported previously. This indicates that either the absolute electronegativity scale (or the absolute hardness one) or a binary scale, or both is very useful in extracting the information desired for various proteins by the present method from the amino acid and the RNA sequence.