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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