Comparison of p-values for the new and old finite-size corrections using the BLOSUM62 scoring matrix and 11 + g affine gap penalty for equal sequence lengths (m=n) 40, 100, 200, and 400. Figure 2 plots against p, where is the calculated p-value and p is the p-value from the simulation. Thus, a perfect p-value estimate corresponds to the horizontal line y = 0. The red line shows the results from the new finite-size correction; the black line, the old finite-size correction.
Park et al. BMC Research Notes 2012 5:286 doi:10.1186/1756-0500-5-286