Skip to main content

Table 1 Comparison of VD and PD/VD performance based on visual inspection of 300 of the top ranked sequences for each proteome

From: An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom

Organism Method TP FP FN FDP (%) S (%)
A. thaliana VD 116 8 0 6.5 100.0
PD/VD 116 4 0 3.3 100.0
S. bicolor VD 105 6 0 5.4 100.0
PD/VD 104 2 1 1.9 99.0
O. sativa VD 90 11 1 10.9 98.9
PD/VD 90 6 1 6.3 98.9
P. patens VD 40 0 3 0.0 93.0
PD/VD 37 0 6 0.0 86.0
P. trichocarpa VD 95 14 3 12.8 96.9
PD/VD 95 11 3 10.4 96.9
V. vinifera VD 80 10 0 11.1 100.0
PD/VD 80 6 0 7.0 100.0
Σ208,298 sequences VD 526 49 7 8.5 98.7
PD/VD 522 29 11 5.3 97.9
  1. The total number of entries in six proteomes and the numbers of GDSL identified by VD and PD/VD as well as respective statistical measures are shown in bold. TP true positive, FP false positive, FN false negative, S sensitivity [S = TP/(TP + FN)], FDP false discovery proportion [FDP = FP/(FP + TP)]; TPs that were eliminated by PD/VD protocol were added to the FN group