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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
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BMC Bioinformatics

ISSN: 1471-2105

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