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Table 5 Fraction of times (in percent) that a specific matrix in the PFASUM MSA Matrices set produced an MSA of at least as good (≥) quality as a specific matrix out of the Standard MSA Matrices set

From: PFASUM: a substitution matrix from Pfam structural alignments

   PFASUM31 PFASUM43 PFASUM60
BAliBASE 3.0 BLOSUM50 67.36 (59.07) 62.69 (54.92) 62.44 (51.81)
  BLOSUM62 71.50 (65.03) 69.43 (62.44) 67.88 (58.03)
  PAM250 75.39 (70.21) 71.76 (63.73) 70.73 (66.84)
  VTML160 63.47 (54.92) 61.14 (50.52) 61.66 (48.45)
  VTML200 68.13 (57.77) 63.21 (51.81) 61.92 (50.00)
OXBench BLOSUM50 81.52 (25.06) 83.29 (26.84) 84.30 (23.80)
  BLOSUM62 79.24 (23.04) 81.01 (22.03) 80.76 (21.52)
  PAM250 80.00 (32.41) 82.03 (31.65) 79.49 (33.16)
  VTML160 79.24 (24.81) 83.80 (28.61) 82.53 (25.32)
  VTML200 76.96 (20.76) 82.03 (22.53) 80.00 (20.51)
SABmark 1.65 BLOSUM50 67.85 (47.52) 63.36 (44.21) 65.96 (43.74)
  BLOSUM62 63.59 (48.23) 64.30 (47.28) 64.30 (45.86)
  PAM250 72.58 (59.57) 70.21 (56.97) 72.81 (60.05)
  VTML160 64.78 (45.39) 60.76 (43.50) 65.25 (42.08)
  VTML200 66.67 (47.99) 63.83 (44.21) 68.56 (44.21)
  1. The comparison for better-than-relations (>) are shown in brackets. Values are shown for all PFASUM MSA Matrices vs. Standard MSA Matrices comparisons on all three different benchmark datasets