|
Comparison of the six algorithms, using the microarray hybridization data from the Sakai sequenced strain. The result of using each algorithm were compared to BLASTN data and are shown below. |
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| Cut-off |
TP |
FP |
TN |
FN |
Sensitivity |
Specificity |
M-Score |
|
|
|
||||||||
| 0.50 |
5285 |
2 |
416 |
41 |
99.23 |
99.52 |
99.25 |
|
| Naïve |
0.33 |
5297 |
6 |
412 |
29 |
99.45 |
98.56 |
99.39 |
| cut-off |
0.25 |
5302 |
8 |
410 |
24 |
99.55 |
98.09 |
99.44 |
| 0.20 |
5308 |
12 |
406 |
18 |
99.66 |
97.13 |
99.48 |
|
| 0.10 |
5316 |
64 |
354 |
10 |
99.81 |
84.69 |
98.71 |
|
|
|
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| GENCOM* |
5238 |
2 |
416 |
88 |
98.34 |
99.52 |
98.43 |
|
|
|
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| GACK** |
EPP = 50 |
5137 |
1 |
417 |
189 |
96.45 |
99.76 |
96.69 |
| EPP= 0 |
5261 |
1 |
417 |
65 |
98.78 |
99.76 |
98.85 |
|
|
|
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| Prowollik |
5277 |
1 |
417 |
49 |
99.07 |
98.76 |
99.13 |
|
|
|
||||||||
| MKD*** |
5297 |
6 |
412 |
29 |
99.45 |
98.56 |
99.39 |
|
|
|
||||||||
| Mixture |
Bimodal |
5296 |
8 |
413 |
30 |
99.44 |
98.80 |
99.39 |
| Trimodal |
5244 |
1 |
417 |
82 |
98.46 |
99.76 |
98.55 |
|
|
The number of genes estimated as correctly conserved (True positives, TP), genes identified as conserved but actually are variable (false positives, FP), genes identified as correctly variable (true negatives TN), and genes identified falsely as variable (false negative FN), are given. The sensitivity, specificity, and M-Score are also calculated, where the sensitivity = TP/(TP+FP), specificity = TN/(FP+TN), and M-Score = Sensitivity*prevalence + Specificity*(1-prevalence) * Institute of Food Research method (GENCOM) ** Genotyping Analysis by Charlie Kim method (GACK) *** Minimum Kernel Density method (MKD) | ||||||||
Carter et al. BMC Genomics 2008 9:53 doi:10.1186/1471-2164-9-53 |
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