Table 1

Impact on alignment quality following refinement.

BAliBASE reference alignments

ClustalW

Dialign

Mafft


Default

RASCAL

RF

REFINER

Default

RASCAL

RF

REFINER

Default

RASCAL

RF

REFINER


Reference 1

0.65

0.63

0.66

0.66

0.62

0.65

0.67

0.62

0.70

0.69

0.69

0.71

Reference 2

0.78

0.80

0.80

0.80

0.78

0.80

0.79

0.79

0.83

0.82

0.83

0.82

Reference 3

0.66

0.69

0.67

0.68

0.65

0.64

0.65

0.66

0.76

0.73

0.75

0.77

Reference 4

0.67

0.68

0.66

0.70

0.67

0.71

0.66

0.69

0.75

0.73

0.70

0.77

Reference 5

0.65

0.67

0.66

0.68

0.67

0.65

0.64

0.67

0.76

0.73

0.72

0.76

Average

0.682

0.694

0.69

0.704

0.678

0.690

0.682

0.692

0.760

0.740

0.738

0.766

Increment (%)

0

1.760

1.173

3.226

0.000

1.770

0.590

2.065

0.000

-2.632

-2.895

0.789


BAliBASE reference alignments

Muscle

Probcons

T-Coffee


Default

RASCAL

RF

REFINER

Default

RASCAL

RF

REFINER

Default

RASCAL

RF

REFINER


Reference 1

0.66

0.66

0.67

0.67

0.72

0.72

0.70

0.73

0.68

0.68

0.69

0.68

Reference 2

0.80

0.81

0.80

0.80

0.83

0.83

0.82

0.82

0.81

0.83

0.82

0.82

Reference 3

0.71

0.71

0.71

0.73

0.76

0.73

0.75

0.77

0.63

0.62

0.62

0.64

Reference 4

0.71

0.72

0.68

0.72

0.77

0.75

0.71

0.77

0.71

0.71

0.70

0.72

Reference 5

0.70

0.71

0.67

0.71

0.76

0.74

0.71

0.75

0.73

0.73

0.69

0.74

Average

0.716

0.722

0.706

0.734

0.768

0.754

0.738

0.77

0.704

0.714

0.704

0.720

Increment (%)

0.000

0.838

-1.397

2.514

0.000

-1.823

-3.906

0.260

0.000

1.420

0.000

2.273


Chakrabarti et al. BMC Bioinformatics 2006 7:499   doi:10.1186/1471-2105-7-499

Open Data