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Table 6 Iterative refinement versus consistency, compared on SABmark

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

  Twilight zone (209) Superfamily (425)
Strategy FD % basic Time (sec) FD % basic Time (sec)
basic 24.05 100.0 1.10 53.74 100.0 0.95
random × 100 25.47 105.9 1.64 54.62 101.6 1.49
tree Random × 100 26.21 109.0 1.51 55.43 103.2 1.30
tree BFS × 100 26.08 108.5 1.19 55.29 102.9 0.98
triplet SeqAn 26.74 111.2 1.97 55.40 103.1 1.60
triplet SeqAn + tree BFS × 100 27.39 113.9 7.35 55.51 103.3 5.75
  1. Columns show the average developer (FD) score, the percentage value of the FD score relative to the basic strategy (%basic) and the average run time achieved by different alignment strategies for the "Superfamily" and "Twilight Zone" sets in the SABmark database. The number of alignments in each reference is given in parentheses. The best results in each column are shown in bold