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Table 2 Comparison of multiple sequence alignment methods

From: MSARC: Multiple sequence alignment by residue clustering

  SP/TC scores Computation
Aligner All RV11 RV12 RV20 RV30 RV40 RV50 BB40037 Time
Non-progressive methods       
MSARC 87.6 57.1 69 . 9 46 . 3 94.5 85.7 92.5 39.2 83.7 47.2 93 . 2 62.3 88.7 51.6 98 . 7 70 . 0 16:36:37
DIALIGN-T 77.3 42.8 49.3 25.3 88.8 72.5 86.3 29.2 74.7 34.9 82.0 45.2 80.1 44.2 52.6 0.0 1:13:21
FSA 78.5 42.1 50.3 26.9 92.4 81.8 86.7 18.7 70.7 27.6 85.5 46.2 78.2 39.8 81.8 30.0 35:15:34
PicXAA 87 . 8 59.4 69.0 46 . 3 94.6 86.2 92.5 41.6 86.0 59.8 93.1 62 . 4 89.2 53.0 98 . 7 70 . 0 5:54:18
Progressive methods       
CLUSTAL Ω 84.0 55.4 59.0 35.8 90.6 78.9 90.2 45.0 86.2 57.5 90.2 57.9 86.2 53.3 61.2 0.0 1 2:1 5
DIALIGN-TX 78.8 44.3 51.5 26.5 89.2 75.2 87.9 30.5 76.2 38.5 83.6 44.8 82.3 46.6 52.8 0.0 1:36:05
MAFFT 86.7 58.4 65.3 42.8 93.6 83.8 92.5 44.6 85.9 58.1 91.5 59.0 90.1 59.4 56.4 0.0 54:04
MSAProbs 87 . 8 60 . 7 68.2 44.1 94 . 6 86 . 5 92 . 8 46 . 4 86 . 5 60 . 7 92.5 62.2 90 . 8 60 . 8 59.5 0.0 6:43:51
MUSCLE 81.9 47.5 57.2 31.8 91.5 80.4 88.9 35.0 81.4 40.9 86.5 45.0 83.5 45.9 48.4 0.0 23:32
Probalign 87.6 58.9 69.5 45.3 94 . 6 86.2 92.6 43.9 85.3 56.6 92.2 60.3 88.7 54.9 54.2 0.0 4:31:41
ProbCons 86.4 55.8 67.0 41.7 94.1 85.5 91.7 40.6 84.5 54.4 90.3 53.2 89.4 57.3 59.3 0.0 6:56:32
T-Coffee 85.7 55.1 65.5 40.9 93.9 84.8 91.4 40.1 83.7 49.0 89.2 54.5 89.4 58.5 50.9 0.0 13:53:02
  1. Columns 2-9 show the mean SP and TC scores for each alignment algorithm on the whole BAliBASE 3.0 dataset, each of its series and case BB40037. The last column presents total CPU computation time (hh:mm:ss). All scores are multiplied by 100. Best results in each column are shown in bold.