Table 1.
Method & params | P.f /P.g | P.f /P.k | P.f /P.v | P.f /P.y | P.k /All | Total Time (Mins) | |||||
---|---|---|---|---|---|---|---|---|---|---|---|
Sen. (%) | Spe. (%) | Sen. (%) | Spe. (%) | Sen. (%) | Spe. (%) | Sen. (%) | Spe. (%) | Sen. (%) | Spe. (%) | ||
XMAligner -hashSize = 20 -binaryHash = true -limit = 500 | |||||||||||
r = 0.15 | 76.44 | 75.94 | 57.61 | 83.53 | 55.94 | 86.21 | 75.81 | 81.49 | 80.12 | 79.71 | 451.62 |
r = 0.25 | 51.83 | 86.50 | 42.03 | 90.81 | 39.60 | 91.65 | 52.22 | 89.45 | 59.73 | 88.63 | 441.40 |
r = 0.35 | 35.37 | 93.55 | 31.13 | 94.54 | 28.76 | 94.58 | 36.11 | 93.92 | 44.08 | 93.31 | 439.53 |
Promer -l 6 -g 30 | |||||||||||
c = 10 | 78.43 | 50.48 | 66.88 | 51.13 | 62.66 | 51.61 | 80.37 | 51.80 | 87.55 | 52.85 | 327.21 |
c = 20 | 46.23 | 78.72 | 43.15 | 89.13 | 39.76 | 92.35 | 48.98 | 83.14 | 54.16 | 79.72 | 33.39 |
c = 40 | 34.38 | 86.36 | 29.83 | 95.92 | 27.13 | 97.32 | 32.92 | 90.01 | 31.14 | 87.89 | 28.23 |
Nucmer -l 14 -g 160 | |||||||||||
c = 40 | 18.94 | 73.82 | 6.64 | 52.99 | 3.61 | 41.80 | 17.54 | 74.50 | 22.12 | 72.79 | 17.76 |
c = 65 | 14.63 | 94.65 | 3.71 | 88.44 | 1.71 | 76.98 | 12.86 | 95.93 | 16.01 | 94.42 | 7.89 |
c = 90 | 11.69 | 97.10 | 2.22 | 87.52 | 0.86 | 73.31 | 10.08 | 97.33 | 12.20 | 96.65 | 6.66 |
Blastz -notransition -step = 20 -nogapped | |||||||||||
t = 3000 | 34.24 | 75.35 | 19.26 | 69.03 | 13.74 | 73.91 | 30.96 | 82.19 | 44.97 | 75.65 | 34.57 |
t = 5000 | 28.16 | 95.56 | 15.51 | 93.58 | 11.43 | 94.55 | 25.82 | 96.43 | 37.89 | 94.78 | 31.23 |
t = 7000 | 24.73 | 96.88 | 14.05 | 96.02 | 10.69 | 95.88 | 23.43 | 97.03 | 33.31 | 96.35 | 30.89 |