Our DNA SAP analyses examined the effects of both the number of target as well as the number of NN sequences, but To discriminate samples in which zero NNs were used, the range is drawn as a horizontal gray line, and when n > 0, the range is drawn as a black line. The best estimate of the true value is the quality measure determined using the entire target and NN pools, and is represented by a vertical black line. This best estimate plus a constant c ¼ 20 is at the location of the vertical dashed line and was selected to indicate a reasonable distance from the true answer. The 75% quantile for each range is shown with a black, vertical tick mark. our protein SAP analyses investigated the effects of only the number of target sequences. This is because composing the lists of NN proteins for random, temporary exclusion from the protein nr database (to estimate the value of that NN sequence data) would be difficult to automate for rapid, high-throughput computations. Thus, we compared the target proteins with all the proteins in nr, regardless of their phylogenetic relationship to the target. This was comparable with DNA SAP results using all available NN data.