TransportTP: A two-phase classification approach for membrane transporter prediction and characterization

BMC Bioinformatics

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.

ISSN: 1471-2105