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Figure 2 | BMC Research Notes

Figure 2

From: New finite-size correction for local alignment score distributions

Figure 2

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. Figure2 plots log 10 p ^ / p against p, where p ^ 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.

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