Table 2

Results of validation on FAMeS Data sets

FAMeS Data set

Taxonomic assignment category

Results with complete database

Results with modified database


INDUS

TACOA

SOrT-ITEMS

MEGAN

SPHINX

INDUS

TACOA

SOrT-ITEMS

MEGAN

SPHINX


SimLC (96732)

Correct

89.6

79.3

94.9

95

93.1

81.6

74.4

78.1

72.6

83.7

Wrong

2.6

9

2

2.7

2.8

7.1

13.9

9.2

23.6

11.5

Specific

81.3

24.4

94.9

93.9

82.8

66.7

21

78.1

65

71

Non-specific

8.3

54.9

0

1.1

10.3

14.9

53.5

0

7.6

12.7

Unassigned

7.9

11.6

3.1

2.3

4.1

11.4

11.6

12.6

3.7

4.8


SimMC (113373)

Correct

92.8

82.5

93.7

94

92.6

86

79

79.1

69.9

81.8

Wrong

1

7.3

3.1

3.5

3.6

4.6

10.8

9.1

26.6

13.5

Specific

84.1

23.7

93.7

93.1

81.1

71.9

23

79.1

63.2

70.1

Non-specific

8.7

58.8

0

1

11.5

14.1

56

0

6.7

11.6

Unassigned

6.2

10.2

3.2

2.4

3.8

9.4

10.2

11.8

3.5

4.7


SimHC (115592)

Correct

89.6

72.1

92

91.9

86

78.9

67

76.6

77.9

77.6

Wrong

1.9

11.4

3.6

4.9

7.1

5.7

16

9.5

17.6

10.1

Specific

76.4

18.7

92

90.3

79.6

63.4

18.2

76.6

69.5

71.2

Non-specific

13.2

53.4

0

1.5

6.4

15.5

48.8

0

8.4

6.4

Unassigned

8.6

16.5

4.3

3.2

6.9

15.5

17

13.9

4.5

12.3


Average for FAMeS data sets

Correct

90.6

78

93.5

93.6

90.6

82.2

73.5

77.9

73.5

81

Wrong

1.8

9.3

2.9

3.7

4.5

5.8

13.6

9.3

22.6

11.7

Specific

80.6

22.3

93.5

92.4

81.2

67.3

20.7

77.9

65.9

70.8

Non-specific

10.1

55.7

0

1.2

9.4

14.8

52.8

0

7.6

10.2

Unassigned

7.6

12.8

3.5

2.6

4.9

12.1

12.9

12.8

3.9

7.3


Summary of the results obtained with the FAMeS metagenomic data sets. The complete and modified reference database contained genome fragments from 952 and 652 prokaryotic genomes respectively. The number of sequences in each data set is indicated in parenthesis.

Mohammed et al. BMC Genomics 2011 12(Suppl 3):S4   doi:10.1186/1471-2164-12-S3-S4

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