The SAP analyses for proteins proceed much like that for DNA signatures. Random samples of size t target sequences are generated, where t ranges from 1 to T, the total number of target sequences in the pool. Either finished data, actual draft data, or draft data simulated as described below are aligned using WGASA. The protein signature prediction pipeline is run on each random sample, and the range, median, 75th and 90th quantiles of the number of protein signature candidates for the samples of a given target size t is plotted in range plots as described above.