Table 4 Independent accuracy measures for AMPS runs on the Master data set at various gap-penalties. Clustering was performed on significance score (from 100 randomisations) with the PAM250 matrix. S c : Scoring method based on STAMP S c [25]. RMSD: Score based on Root Means Squared Deviation. Pfit: Percentage of aligned positions without gap used in fit.
From: OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy
Gap-penalty | S c | p | RMSD | p | Pfit |
|---|---|---|---|---|---|
0 | 7.082 | <2.2e-16 | 3.342 | <2.2e-16 | 92.52 |
3 | 7.208 | 2.213e-05 | 3.176 | 0.0001652 | 93.28 |
6 | 7.238 | 0.1558 | 3.145 | NA | 93.50 |
9 | 7.245 | NA | 3.156 | 0.807 | 93.62 |
12 | 7.239 | 0.01863 | 3.152 | 0.7806 | 93.69 |
15 | 7.221 | 0.0006053 | 3.151 | 0.2370 | 93.77 |
18 | 7.192 | 1.481e-07 | 3.189 | 0.02599 | 93.82 |
21 | 7.169 | 7.09e-ll | 3.211 | 0.002619 | 93.85 |
24 | 7.144 | 4.038e-15 | 3.230 | 0.0001391 | 93.88 |
27 | 7.111 | <2.2e-16 | 3.304 | 5.281e-07 | 93.92 |
30 | 7.081 | <2.2e-16 | 3.333 | 1.044e-08 | 93.95 |