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Table 9 Performance of aligners on the PREFAB benchmark

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

  Identity range (main set)  
Aligner 0-0.2 (1104) 0.2-0.4 (400) 0.4-0.7 (109) 0.7-1 (69) Overall (1682) Time(sec)
MMSA 0.58 0.88 0.98 0.98 0.69 21.47
ProbCons 0.61 0.90 0.97 0.98 0.72 46.68
T-Coffee 0.60 0.89 0.97 0.98 0.71 110.66
MUSCLE 0.56 0.88 0.97 0.98 0.68 2.00
MAFFT 0.62 0.90 0.98 0.98 0.72 4.16
ClustalW 0.48 0.84 0.98 0.99 0.62 4.83
ClustalO 0.584 0.895 0.976 0.987 0.700 1.419
Kalign 0.525 0.845 0.977 0.984 0.649 0.160
MSAProbs 0.635 0.913 0.974 0.979 0.737 49.192
  Identity range (weighted set)  
Aligner 0-0.2 (59) 0.2-0.4 (30) 0.4-0.7 (4) 0.7-1 (7) Overall (100) Time(sec)
MMSA 0.43 0.82 0.96 0.98 0.60 2.82
ProbCons 0.50 0.87 0.93 0.99 0.66 14.18
T-Coffee 0.46 0.75 0.93 0.99 0.60 33.74
MUSCLE 0.42 0.84 0.95 0.99 0.61 1.32
MAFFT 0.46 0.87 0.96 0.99 0.64 1.31
ClustalW 0.39 0.88 0.96 0.99 0.60 1.60
ClustalO 0.488 0.876 0.964 0.989 0.658 1.107
Kalign 0.435 0.876 0.963 0.989 0.627 0.114
MSAProbs 0.484 0.881 0.964 0.990 0.658 12.660
  1. Columns show the average Q (equivalent to SP) score achieved for subsets of PREFAB benchmark database, that correspond to different identity values of the structural pair. The number of alignments in each identity range is given in parenthesis. Overall average scores and run time are given in the last two columns. Values for the main and weighted sets are given separately. The best results in each column are shown in bold