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Table 4 Comparing score transformation strategies on SABmark

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

Strategy

Twilight zone (209)

Superfamily (425)

 

FD

% basic

Time (sec)

FD

% basic

Time (sec)

basic

24.05

100.0

1.10

53.74

100.0

0.95

triplet T-Coffee

24.83

103.3

1.10

54.30

101.0

0.90

triplet SeqAn

26.74

111.2

1.97

55.40

103.1

1.60

triplet SeqAn × 2

25.87

107.6

17.38

55.45

103.2

14.39

triplet SeqAn × 3

20.78

86.4

77.65

50.77

94.5

68.59

clique

20.05

83.4

7.63

48.66

90.5

6.35

triplet T-Coffee + clique

25.28

105.1

9.54

54.65

101.7

7.97

triplet SeqAn + clique

25.36

105.4

11.55

54.46

101.3

7.90

maxflow + clique

21.82

90.7

10.34

52.02

96.8

8.70

  1. Columns show the average developer (FD) score, the percentage value of the FD score relative to the basic strategy (%basic) and the average run time achieved by different alignment strategies for the "Superfamily" and "Twilight Zone" sets in the SABmark database. The number of sequences in each reference is given in parentheses. The best results in each column are shown in bold
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BMC Bioinformatics

ISSN: 1471-2105

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