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Table 2 BLAST sequence homology search results within TC families in 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 [%]

83.3

84.4

86.7

90.0

60.3

78.6

79.6

79.6

87.8

64.1

84.7

85.4

97.5

97.5

54.1

Recall [%]

83.3

84.4

86.7

90.0

76.2

78.6

79.6

79.6

87.8

65.1

84.7

85.4

97.5

97.5

62.9

F-measure[%]

83.3

84.4

86.7

90.0

64.7

78.6

79.6

79.6

87.8

63.6

84.7

85.4

97.5

97.5

55.2

Unclassified [%]

82.2

52.2

37.8

25.6

0.0

56.1

44.9

40.8

29.6

0.0

48.4

43.3

35.0

19.1

0.0

  1. Accuracy measures of the BLAST prediction results for finding homologous transporter pairs in the Ec-At, Ec-Sc, and Sc-At comparison that belong to the same TC family for various E-value thresholds. The results were normalized by the size of the reference database (see text). Both precision and recall have a peak at thresholds 1e-12 or 1e-8 but showed lower accuracies under other thresholds. The unclassified percentage decreases as the thresholds’ values increase.
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BMC Bioinformatics

ISSN: 1471-2105

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