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Table 1 BRAliBase Cline scores

From: ReformAlign: improved multiple sequence alignments using a profile-based meta-alignment approach

APSI [25%-100%] (N = 2,218)

Aligner

Initial (I)

Reformed (R)

Avg. Dif. (R-I)

p-value

R > I

R = I

R < I

ClustalW

84.97%

86.09%

1.12%

p < 0.001***

40.22%

46.71%

13.07%

ClustalO

85.41%

87.71%

2.30%

p < 0.001***

44.00%

40.76%

15.24%

Kalign

89.30%

89.61%

0.30%

p < 0.001***

36.29%

46.93%

16.77%

Mafft (FFTnsi)

89.16%

89.94%

0.78%

p < 0.001***

27.23%

57.35%

15.42%

Mafft (Linsi)

88.63%

89.33%

0.70%

p < 0.001***

27.46%

55.91%

16.64%

Muscle

89.68%

89.89%

0.21%

p < 0.001***

21.51%

63.53%

14.97%

DialignTX

81.17%

84.82%

3.65%

p < 0.001***

54.78%

35.21%

10.01%

GramAlign

80.47%

84.90%

4.43%

p < 0.001***

54.64%

37.29%

8.07%

ProbCons

91.35%

91.34%

−0.01%

p = 0.127

27.41%

42.34%

30.25%

PicXAA

91.51%

91.46%

−0.06%

p < 0.001***

26.28%

41.88%

31.83%

R-Coffee

91.34%

91.42%

0.08%

p < 0.001***

39.18%

32.33%

28.49%

APSI [25%-55%] (N = 869)

Aligner

Initial (I)

Reformed (R)

Avg. Dif. (R-I)

p-value

R > I

R = I

R < I

ClustalW

69.03%

71.57%

2.54%

p < 0.001***

71.00%

14.04%

14.96%

ClustalO

69.19%

74.82%

5.63%

p < 0.001***

79.29%

3.68%

17.03%

Kalign

79.32%

79.95%

0.63%

p < 0.001***

53.28%

22.09%

24.63%

Mafft (FFTnsi)

78.46%

80.35%

1.89%

p < 0.001***

53.51%

23.82%

22.67%

Mafft (Linsi)

77.79%

79.38%

1.59%

p < 0.001***

48.10%

26.12%

25.78%

Muscle

79.79%

80.33%

0.54%

p < 0.001***

42.58%

34.52%

22.90%

DialignTX

59.75%

68.31%

8.56%

p < 0.001***

90.33%

0.69%

8.98%

GramAlign

66.63%

70.10%

3.47%

p < 0.001***

78.02%

11.85%

10.13%

ProbCons

83.39%

83.39%

0.00%

p = 0.581

42.58%

10.01%

47.41%

PicXAA

83.77%

83.67%

−0.10%

p = 0.001***

40.05%

9.21%

50.75%

R-Coffee

83.67%

83.57%

−0.10%

p = 0.429

46.49%

4.83%

48.68%

APSI [55%-75%] (N = 284)

Aligner

Initial (I)

Reformed (R)

Avg. Dif. (R-I)

p-value

R > I

R = I

R < I

ClustalW

84.78%

85.40%

0.62%

p < 0.001***

48.94%

25.35%

25.70%

ClustalO

87.53%

87.91%

0.38%

p = 0.001***

49.30%

11.62%

39.08%

Kalign

86.37%

86.76%

0.39%

p < 0.001***

55.28%

25.35%

19.37%

Mafft (FFTnsi)

87.46%

87.76%

0.30%

p = 0.004**

34.51%

37.32%

28.17%

Mafft (Linsi)

86.65%

86.80%

0.15%

p = 0.875

28.87%

39.08%

32.04%

Muscle

87.80%

87.80%

0.00%

p = 0.905

25.35%

46.48%

28.17%

DialignTX

83.49%

85.25%

1.76%

p < 0.001***

73.59%

5.63%

20.77%

GramAlign

81.75%

83.78%

2.03%

p < 0.001***

73.94%

17.25%

8.80%

ProbCons

89.23%

89.26%

0.03%

p = 0.686

41.20%

19.72%

39.08%

PicXAA

89.34%

89.33%

−0.01%

p = 0.609

39.08%

21.83%

39.08%

R-Coffee

89.49%

89.59%

0.10%

p = 0.014*

48.94%

11.27%

39.79%

APSI [75%-90%] (N = 840)

Aligner

Initial (I)

Reformed (R)

Avg. Dif. (R-I)

p-value

R > I

R = I

R < I

ClustalW

98.16%

98.26%

0.10%

p < 0.001***

12.02%

81.79%

6.19%

ClustalO

98.20%

98.30%

0.10%

p < 0.001***

13.69%

80.36%

5.95%

Kalign

98.40%

98.41%

0.01%

p = 0.074

13.21%

77.62%

9.17%

Mafft (FFTnsi)

98.52%

98.51%

−0.01%

p = 0.178

3.93%

90.95%

5.12%

Mafft (Linsi)

98.08%

98.23%

0.15%

p < 0.001***

10.83%

85.60%

3.57%

Muscle

98.41%

98.41%

0.00%

p = 0.489

3.57%

92.38%

4.05%

DialignTX

98.15%

98.30%

0.15%

p < 0.001***

20.24%

72.86%

6.90%

GramAlign

92.78%

97.35%

4.57%

p < 0.001***

27.14%

66.07%

6.79%

ProbCons

98.61%

98.57%

−0.04%

p < 0.001***

8.33%

78.81%

12.86%

PicXAA

98.61%

98.58%

−0.03%

p < 0.001***

8.93%

77.62%

13.45%

R-Coffee

98.27%

98.48%

0.21%

p < 0.001***

27.74%

64.52%

7.74%

APSI [95%-100%] (N = 225)

Aligner

Initial (I)

Reformed (R)

Avg. Dif. (R-I)

p-value

R > I

R = I

R < I

ClustalW

97.53%

97.59%

0.06%

p = 0.030*

15.56%

68.89%

15.56%

ClustalO

97.62%

97.66%

0.04%

p = 0.245

14.22%

72.89%

12.89%

Kalign

97.57%

97.63%

0.06%

p < 0.001***

32.89%

55.56%

11.56%

Mafft (FFTnsi)

97.72%

97.70%

−0.02%

p = 0.009**

3.56%

86.67%

9.78%

Mafft (Linsi)

97.67%

97.73%

0.06%

p = 0.642

8.00%

81.33%

10.67%

Muscle

97.68%

97.67%

−0.01%

p = 0.011*

2.22%

89.33%

8.44%

DialignTX

97.58%

97.69%

0.11%

p < 0.001***

22.67%

65.33%

12.00%

GramAlign

86.28%

96.95%

10.67%

p < 0.001***

42.67%

53.33%

4.00%

ProbCons

97.66%

97.67%

0.01%

p = 0.299

22.67%

59.56%

17.78%

PicXAA

97.67%

97.68%

0.01%

p = 0.526

21.78%

60.00%

18.22%

R-Coffee

97.41%

97.68%

0.27%

p < 0.001***

41.33%

44.89%

13.78%

  1. Cline scores corresponding to the 2,218 alignments of the BRAliBase dataset. *significant at p<0.05, **significant at p<0.005, ***significant at p≤0.001. The first sub-table summarizes the performance of each alignment pair averaged over all test cases whereas the remaining sub-tables report the results organized according to the average pairwise sequence identity of the sequences. For every sub-table, the APSI value and the number of alignments (N) corresponding to each group are reported in the first row. Columns 2 and 3 correspond to the average Cline scores of the initial (I) and the reformed (R) alignments respectively. The average differences (R-I) per alignment pair are given in the fourth column and the corresponding p-values of these differences are given at the fifth column (statistically significant values at the .05 significance level are highlighted in bold). Finally, columns 6–8 indicate the percentage of cases where the reformed alignments were superior, equal or inferior (in terms of Cline score) to the initial alignment.
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BMC Bioinformatics

ISSN: 1471-2105

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