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
| 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) |
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