Table 3

Case study results of TransportTP on five plant organisms.

Organism

Curated

Predicted

Matches

Recall (%)

Precision (%)

Potential rate(%)

S. Bicolor

1918

1960

1485

77.4

75.8

7.7

P. trichocarpa

2512

2889

1936

77.1

67.0

14.4

V. vinifera

2188

2002

1540

70.4

76.9

5.5

P. patens

1388

1380

1019

73.4

73.8

6.8

average

74.6

73.4

8.6

C. reinhardtii

979

770

554

56.6

71.9

7.7

The manual curation and automatic prediction by TransportTP were compared in five plant organisms at the e-value threshold of 10. The column of curated is the number of transporters manually curated with confidence level 1 or level 2. The fourth column corresponds to the number of predictions matched the curation with confidence levels 1 and 2. The last column is the proportion of predictions matched the curation with confidence level 3.

Li et al. BMC Bioinformatics 2009 10:418   doi:10.1186/1471-2105-10-418