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Table 3 HMMER results for homology between TC families from the three organisms

From: Transferring functional annotations of membrane transporters on the basis of sequence similarity and sequence motifs

 

Ec- At

Ec- Sc

Sc- At

1e-20

1e-16

1e-12

1e-8

1e-4

1e-20

1e-16

1e-12

1e-8

1e-4

1e-20

1e-16

1e-12

1e-8

1e-4

Precision [%]

73.3

85.6

86.7

90.0

90.8

78.6

78.6

81.6

86.7

92.9

84.7

85.4

85.4

97.5

93.7

Recall [%]

73.3

85.6

86.7

90.0

92.1

78.6

78.6

81.6

86.7

92.9

84.7

85.4

85.4

97.5

96.0

F-measure[%]

73.3

85.6

86.7

90.0

91.4

78.6

78.6

81.6

86.7

92.9

84.7

85.4

85.4

97.5

94.7

Unclassified [%]

76.7

52.2

40.0

33.3

17.8

21.4

21.4

18.4

13.3

7.1

15.3

14.6

14.6

2.5

2.5

  1. HMMER prediction results (sequence E-values) under the given E-value confidence thresholds. The results were normalized by the size of the reference database (see text). HMMER gave a better accuracy under loose thresholds compared to BLAST.
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BMC Bioinformatics

ISSN: 1471-2105

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