Figure 1
From: Evolutionary hierarchies of conserved blocks in 5'-noncoding sequences of dicot rbcS genes
Comparison of phylogenetic footprinting tools in predicting the 12 most frequent blocks in the 27 dicot rbcS 5'-NCS. See text for Sensitivity (equation 1) and PPV (equation 2) performance parameters. MOTIF SAMPLER was run 8 times each for background model orders 0–3, and with the prior probability of motif (p) at 0.3, the empirical value from the analytical consensus. Other option settings were s 0, M 1, n 3, w 11, x 0, r 5. Gap penalties for CLUSTALW (1) were: opening 15.0, extension 6.66; and for ALIGN-M and CLUSTALW (2): opening 8.0, extension 0.5. Mean performance parameters shown with standard deviation bars. Values sharing alphabet labels were not significantly different (Mann-Whitney U test, P > 0.05).