Table 3 PRA scores of various alignment methods for the Balibase subsets. Average PRA and percentage of aligned residues (in brackets) for several alignment methods on Balibase3. The average scores for all of the 12 alignment methods is given in the middle row (bold).
From: Automatic extraction of reliable regions from multiple sequence alignments
Set 11 | Set 12 | Set 20 | Set 30 | Set 40 | Set 50 | |
|---|---|---|---|---|---|---|
Kalign | 40.4 (91) | 80.4 (94) | 75.8 (94) | 68 (92) | 61.9 (89) | 65.5 (89) |
ClustalW | 36.4 (97) | 76.2 (96) | 73.5 (95) | 61.8 (94) | 58.9 (92) | 57.2 (93) |
Muscle | 41.8 (93) | 80.6 (95) | 76.3 (96) | 68.5 (94) | 62.6 (92) | 64.4 (92) |
Muscle_maxiters1 | 37.6 (91) | 76.7 (95) | 76.0 (95) | 66.5 (93) | 59.9 (91) | 60.1 (91) |
Muscle_maxiters2 | 39.2 (92) | 78.5 (95) | 76.0 (95) | 67.7 (93) | 61.8 (91) | 62.9 (90) |
G-INS-1 | 41.8 (87) | 79.6 (94) | 77.1 (94) | 70.9 (91) | 63.9 (88) | 66.0 (89) |
G-INS-i | 44.7 (90) | 81.1 (94) | 78.1 (94) | 71.8 (92) | 64.8 (91) | 68.1 (90) |
L-INS-1 | 47.4 (89) | 81.2 (94) | 78.8 (93) | 72.3 (92) | 66.9 (89) | 68.2 (89) |
L-INS-i | 50.3 (90) | 82.7 (95) | 79.8 (94) | 73.1 (93) | 68.1 (90) | 69.7 (90) |
Dialign | 45.8 (72) | 78.3 (91) | 79.4 (88) | 68.8 (85) | 68.0 (79) | 68.0 (81) |
Probcons | 49.8 (88) | 83.3 (94) | 79.8 (92) | 72.9 (90) | 69.0 (85) | 71.6 (85) |
Poa | 46.3 (52) | 78.5 (84) | 75.3 (89) | 62.9 (87) | 63.6 (79) | 58.2 (82) |
Average | 43.5 (86) | 79.7 (93) | 77.2 (93) | 68.8 (91) | 64.1 (88) | 65.0 (88) |
Mumsa (f = 1) | 34.5 (93) | 72.6 (93) | 72.8 (94) | 59.5 (91) | 57 (90) | 53.8 (90) |
Mumsa (f = 2) | 48.8 (73) | 83.4 (85) | 81.5 (86) | 75.1 (81) | 71.6 (76) | 73.5 (77) |
Mumsa (f = 3) | 61.5 (49) | 89.0 (78) | 89.4 (77) | 84.8 (68) | 85.5 (60) | 85.4 (60) |
Mumsa (f = 4) | 71.5 (39) | 92.0 (74) | 92.0 (72) | 87.8 (64) | 87.9 (58) | 87.9 (59) |
Mumsa (f = 5) | 74.2 (34) | 93.0 (73) | 92.6 (72) | 90.6 (62) | 90.4 (54) | 91.2 (55) |
Mumsa (f = 6) | 74.4 (29) | 94.9 (67) | 93.5 (70) | 92.3 (58) | 91.7 (53) | 92.5 (52) |
Mumsa (f = 7) | 80.7 (27) | 95.4 (66) | 94.3 (69) | 94.2 (55) | 92.9 (50) | 93.3 (50) |
Mumsa (f = 8) | 79.9 (24) | 96.2 (63) | 95.1 (67) | 93.7 (55) | 93.4 (49) | 94.0 (49) |
Mumsa (f = 9) | 80.3 (23) | 96.2 (63) | 94.9 (67) | 94.5 (55) | 93.9 (48) | 94.5 (47) |
Mumsa (f = 10) | 85.1 (21) | 96.7 (62) | 95.4 (66) | 96.3 (50) | 94.9 (46) | 95.3 (45) |
Mumsa (f = 11) | 82.8 (18) | 97.2 (59) | 96.1 (63) | 97.4 (47) | 94.2 (44) | 96.4 (42) |
Mumsa (f = 12) | 84.9 (13) | 97.9 (53) | 96.5 (60) | 97.9 (43) | 95.8 (39) | 97.0 (37) |