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Table 1 Sensitivity and specificity of exon detection from the P. falciparum genome

From: A genome alignment algorithm based on compression

Method & params

P.f/P.g

P.f/P.k

P.f/P.v

P.f/P.y

P.k/All

Total Time (Mins)

 

Sen. (%)

Spe. (%)

Sen. (%)

Spe. (%)

Sen. (%)

Spe. (%)

Sen. (%)

Spe. (%)

Sen. (%)

Spe. (%)

 

XMAligner -hashSize = 20 -binaryHash = true -limit = 500

r = 0.15

76.44

75.94

57.61

83.53

55.94

86.21

75.81

81.49

80.12

79.71

451.62

r = 0.25

51.83

86.50

42.03

90.81

39.60

91.65

52.22

89.45

59.73

88.63

441.40

r = 0.35

35.37

93.55

31.13

94.54

28.76

94.58

36.11

93.92

44.08

93.31

439.53

Promer -l 6 -g 30

c = 10

78.43

50.48

66.88

51.13

62.66

51.61

80.37

51.80

87.55

52.85

327.21

c = 20

46.23

78.72

43.15

89.13

39.76

92.35

48.98

83.14

54.16

79.72

33.39

c = 40

34.38

86.36

29.83

95.92

27.13

97.32

32.92

90.01

31.14

87.89

28.23

Nucmer -l 14 -g 160

c = 40

18.94

73.82

6.64

52.99

3.61

41.80

17.54

74.50

22.12

72.79

17.76

c = 65

14.63

94.65

3.71

88.44

1.71

76.98

12.86

95.93

16.01

94.42

7.89

c = 90

11.69

97.10

2.22

87.52

0.86

73.31

10.08

97.33

12.20

96.65

6.66

Blastz -notransition -step = 20 -nogapped

t = 3000

34.24

75.35

19.26

69.03

13.74

73.91

30.96

82.19

44.97

75.65

34.57

t = 5000

28.16

95.56

15.51

93.58

11.43

94.55

25.82

96.43

37.89

94.78

31.23

t = 7000

24.73

96.88

14.05

96.02

10.69

95.88

23.43

97.03

33.31

96.35

30.89