Table 5.
The performance of AMPS on the Master data set with 1987 defaults (PAM250, open gap-penalty 8, single order) and optimised (BLOSUM75, gap-penalty 10, tree order) parameters. Percentage SCR is the percentage of residues in the structurally conserved regions. AccSCR : accuracy of alignment in SCRs. p : Wilcoxon Signed Rank test probability
| PID Average 1 | Number of Families 2 | Percentage SCR 3 | AccSCR (PAM250/8) 4 | AccSCR (BLOSUM75/10) 5 | Difference (5–4) | P |
| 0–10 | 21 | 40.5 | 18.3 | 22.2 | 3.9 | 0.0571 |
| 10–20 | 57 | 45.4 | 55.9 | 60.2 | 4.3 | 0.0427 |
| 20–30 | 64 | 54.1 | 76.1 | 81.3 | 5.2 | 0.00214 |
| 30–50 | 175 | 68.6 | 91.3 | 92.3 | 1.0 | 0.00404 |
| 50–100 | 355 | 87.8 | 98.8 | 98.9 | 0.1 | 0.000196 |
| Total | 672 | 74.5 | 88.5 | 89.9 | 1.4 | 7.4e-09 |