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Table 3 Dependent measure accuracies (i.e. comparison of test to reference alignment) for AMPS run on the Master data set at various gap-penalties sorted by Acc SCR – Clustering was performed on SD score (from 100 randomisations) with the PAM250 matrix. Acc SCR : Accuracy of Structurally Conserved Regions. AC a : Accuracy average (pairwise). AC w : Accuracy of whole alignment. PSE : Position Shift Error. NA in columns marked p indicates the highest accuracy in the preceding column, p gives the Wilcoxon Signed Rank test probability that the difference to the highest scoring row occured by chance.

From: OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy

Gap-penalty Acc SCR p AC a p AC w p PSE p
9 88.60 NA 82.30 0.1 74.29 0.09082 0.99 0.8841
12 88.48 0.46 82.49 NA 74.52 NA 0.96 NA
6 88.31 0.032 81.77 6.3e-05 73.64 7.076e-07 1.02 0.9658
15 88.08 0.031 82.31 0.13 74.34 0.2743 0.97 0.0956
3 87.47 5.7e-09 80.39 <2.2e-16 71.82 <2.2e-16 0.98 0.1704
18 87.44 9.0e-05 81.89 0.00020 73.82 0.0002315 1.01 0.000374
21 87.06 5.6e-07 81.68 4.2e-06 73.49 2.507e-07 1.02 4.4e-06
24 86.53 1.8e-10 81.30 5.5e-10 73.00 1.972e-10 1.04 7.565e-08
27 86.02 4.9e-13 80.97 7.6e-12 72.58 1.132e-13 1.12 5.164e-12
30 85.40 <2.2e-16 80.50 6.4e-16 71.85 <2.2e-16 1.17 1.94e-13
0 84.71 <2.2e-16 77.16 <2.2e-16 67.40 <2.2e-16 1.04 1.103e-13