Table 5.
Performance of aligners on the SABmark sequence and structure alignment benchmark
|
|
Superfamily (462) |
Twilight zone (236) |
Overall (698) |
|
||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Aligner
|
fD |
fM |
fD |
fM |
fD |
fM |
Time (mm:ss)
|
|||
| Align-m | 44.4 | 58.9 | 17.1 | 43.0 | 35.2 | 53.5 | 56:44 | |||
| DIALIGN | 50.3 | 42.5 | 22.5 | 19.2 | 41.0 | 34.6 | 8:28 | |||
| CLUSTALW | 53.7 | 38.7 | 24.8 | 15.2 | 43.9 | 30.8 | 2:16 | |||
| MAFFT | 54.1 | 40.0 | 24.8 | 16.0 | 44.2 | 31.9 | 7:33 | |||
| T-Coffee | 55.4 | 41.8 | 26.4 | 18.0 | 45.6 | 33.7 | 59:10 | |||
| MUSCLE | 55.9 | 40.1 | 27.6 | 17.5 | 46.4 | 33.0 | 20:42 | |||
| ProbCons | 59.9 | 45.0 | 32.1 | 21.7 | 50.5 | 37.1 | 17:20 | |||
| ProbCons-ext
|
59.9
|
45.3
|
32.0
|
22.1
|
50.5
|
37.5
|
23:10
|
|||
-
Columns show the average developer (fD) score (equivalent to sum-of-pairs [SP] score) and modeler (fM) score achieved by each aligner for the “Superfamily” and “Twilight Zone” sets in the SABmark database. All scores have been multiplied by 100. The number of sequences in each set is given in parentheses. Overall numbers for the entire database are reported in addition to the total running time of each aligner for all 698 alignments. The best results in each column are shown in bold.
