Generation of the weak synthetic sequence data
To test the sensitivity and specificity of PhyloScan when seeking binding sites that are weaker than E. coli Crp binding sites, we generated "1/2-strength" and "1/3-strength" Crp sites. The 1/2-strength Crp motif was designed to have an average information content per column that is half the average information content of the full-strength Crp motif; we did this by raising each probability of a nucleotide to its 0.637th power, with subsequent scaling so that the probabilities of the four nucleotides for any motif column sum to 1.0. Likewise, the 1/3-strength Crp sites were generated from a 1/3-strength Crp motif to give one-third the average information content, using an exponent of 0.507. See Figure 1 and its legend for more information.