Additional File 2 Direct vs 2-Stage Approaches to Structured Motif Finding

We generated datasets using, for each dataset, a xed template (`, e) for each box. The value of ` varied from 9 to 15 in di erent experiments, with e ∈ {1..b1/3`c}, and with the number of boxes ranging from 2 to 10. For each choice of the parameters we performed 20 runs for each tool, computing the average running time and the corresponding 95% con dence interval. As a general conclusion we may notice that, under these experimental conditions, SISMA tools outperformed the competitors in essentially all datasets on which tools ended comutation within the imposed deadline. Figure 1 reports the results obtained for the pairs (10, 3), (11, 3), (12, 3), (13, 3), and (15, 5) (vertical bars represent the 95% con dence interval of the average running times). Such pairs are typical of the observed behaviors of the four tools within this experimental setting. For what concerns the direct tool comparison, we can make the following observations.