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Table 2 Performance of rank-flexible classifiers on 1000 bp query fragments

From: Classifying short genomic fragments from novel lineages using composition and homology

 

Ge

   

Or

   

Cl

   

Ph

   
 

Sn

FNr

Sp

Ur

Sn

FNr

Sp

Ur

Sn

FNr

Sp

Ur

Sn

FNr

Sp

Ur

TACOA

8.3

0.7

91.6

91.0

15.0

1.3

86.1

83.6

18.5

1.2

93.7

80.3

31.2

4.3

87.9

64.4

PhyloPythiaS

35.2

1.6

94.3

63.2

48.8

3.5

92.7

47.7

56.9

4.1

92.8

39.0

58.7

5.6

93.5

35.7

ε-NB (none) a

95.5

2.6

97.9

2.0

96.2

2.5

98.2

1.4

96.7

2.2

98.2

1.0

97.4

1.9

98.8

0.8

ε-NB (strain) b

92.6

4.5

97.5

3.0

92.2

5.1

96.7

2.8

92.3

5.0

96.4

2.7

92.1

5.2

97.5

2.8

ε-NB (species) c

71.0

17.0

84.5

12.0

73.0

16.6

86.2

10.4

75.4

15.7

87.6

8.9

74.8

16.8

89.7

8.4

LCA (strain)b

96.2

0.8

99.3

3.0

95.8

0.9

99.1

3.3

95.4

0.8

99.3

3.9

95.2

0.9

99.3

4.0

LCA (species)c

82.9

4.1

95.5

13.0

85.2

2.4

97.5

12.4

85.6

1.8

98.0

12.6

85.9

1.7

98.7

1.7

LCA+NB (strain) b

91.5

0.1

99.9

8.4

91.0

0.1

99.8

8.9

90.8

0.1

99.9

9.13

90.8

0.1

100

9.1

LCA+NB (species) c

66.9

0.5

99.2

32.6

69.1

0.3

99.5

30.6

70.9

0.2

99.8

28.9

70.4

0.4

99.9

29.2

  1. ε-NB results are for ε = 105; LCA and LCA+NB results are for E-value < 10-5, p = 15%. Ge = genus, Or = order, Cl = class, Ph = phylum
  2. a no models excluded from training set; b strain-level lineages excluded from training set; c species-level lineages excluded from training set.
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BMC Bioinformatics

ISSN: 1471-2105

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