Table 2 Sensitivity and specificity of exon detection from the P. knowlesi genome
Method & params | P.k/P.f | P.k/P.g | P.k/P.v | P.k/P.y | P.k/All | Total time (Mins) | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Â | Sen. (%) | Spe. (%) | Sen. (%) | Spe. (%) | Sen. (%) | Spe. (%) | Sen. (%) | Spe. (%) | Sen. (%) | Spe. (%) | Â |
XMAligner -hashSize = 20 -binaryHash = true-limit = 500 | |||||||||||
r = 0.15 | 91.73 | 51.62 | 89.04 | 52.50 | 98.23 | 51.48 | 90.74 | 52.68 | 98.77 | 50.57 | 470.40 |
r = 0.25 | 61.82 | 63.02 | 52.38 | 64.83 | 93.49 | 57.09 | 59.61 | 66.42 | 93.30 | 57.06 | 450.56 |
r = 0.35 | 42.12 | 82.86 | 34.05 | 84.74 | 90.01 | 62.06 | 40.78 | 85.89 | 88.64 | 63.87 | 446.37 |
Promer -l 6 -g 30 | |||||||||||
c = 10 | 60.32 | 60.80 | 47.52 | 58.10 | 94.49 | 54.89 | 57.67 | 63.35 | 94.89 | 54.28 | 109.48 |
c = 20 | 45.55 | 90.53 | 37.44 | 91.90 | 92.11 | 67.16 | 43.62 | 91.82 | 92.07 | 67.64 | 41.37 |
c = 40 | 32.40 | 95.28 | 28.60 | 96.46 | 85.67 | 79.62 | 30.40 | 95.50 | 84.60 | 80.12 | 33.99 |
Nucmer -l 14 -g 160 | |||||||||||
c = 40 | 6.31 | 69.61 | 6.36 | 74.28 | 71.59 | 60.98 | 6.31 | 75.44 | 70.84 | 61.14 | 14.05 |
c = 65 | 3.38 | 75.40 | 3.51 | 81.34 | 64.98 | 63.26 | 3.33 | 77.86 | 63.71 | 63.73 | 9.96 |
c = 90 | 1.80 | 74.80 | 1.93 | 83.34 | 58.74 | 65.22 | 1.82 | 80.71 | 57.16 | 65.76 | 8.26 |
Blastz -notransition -step = 20 -nogapped | |||||||||||
t = 3000 | 17.12 | 75.97 | 15.21 | 77.42 | 74.92 | 72.89 | 16.87 | 79.64 | 75.94 | 72.01 | 24.04 |
t = 5000 | 16.24 | 83.96 | 14.62 | 82.64 | 74.29 | 77.23 | 16.10 | 86.48 | 75.06 | 76.59 | 21.04 |
t = 7000 | 15.55 | 87.05 | 14.20 | 85.75 | 73.40 | 81.31 | 15.43 | 89.03 | 73.97 | 80.70 | 20.57 |