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Table 3 Comparing score transformation strategies on BAliBASE

From: Comprehensive comparison of graph based multiple protein sequence alignment strategies

  RV11 (38) RV12 (44) RV20 (41) RV30 (30) RV40 (49) RV50 (16) Overall (218)  
Strategy SP %basic SP %basic SP %basic SP %basic SP %basic SP %basic SP %basic Time (sec)
basic 0.587 100.0 0.908 100.0 0.902 100.0 0.832 100.0 0.884 100.0 0.871 100.0 0.831 100.0 24.44
maxflow 0.585 99.6 0.910 100.2 0.909 100.8 0.836 100.4 0.895 101.2 0.880 100.9 0.836 100.6 25.04
triplet T-Coffee 0.613 104.4 0.914 100.6 0.914 101.3 0.840 100.9 0.901 101.9 0.888 101.9 0.845 101.7 27.85
triplet SeqAn 0.642 109.3 0.929 102.3 0.918 101.8 0.839 100.8 0.911 103.1 0.895 102.7 0.856 103.0 44.83
triplet SeqAn × 2 0.648 110.3 0.928 102.2 0.917 101.7 0.842 101.1 0.910 103.0 0.896 102.8 0.857 103.1 608.79
clique 0.530 90.2 0.896 98.7 0.820 90.9 0.614 73.7 0.758 85.8 0.675 77.4 0.715 86.1 1764.83
triplet T-Coffee + clique 0.637 108.4 0.930 102.4 0.919 101.8 0.839 100.8 0.905 102.4 0.885 101.6 0.852 102.6 1753.63
maxflow + clique 0.590 100.4 0.924 101.8 0.904 100.2 0.819 98.3 0.876 99.1 0.879 100.8 0.832 100.1 2337.67
  1. Columns show the average sum-of-pairs (SP) score and the percentage value of the SP score relative to the basic strategy (%basic) achieved by each alignment strategy for each of the six BAliBASE references. The number of alignments in each reference is given in parentheses. Overall values for the entire database are reported in addition to the mean execution time of each strategy. The best results in each column are shown in bold