Table 2 Non-coding RNA detection using SVMs in comparing the stem kernels with the local alignment kernels.
From: Directed acyclic graph kernels for structural RNA analysis
| Â | Â | Â | Stem kernels | Local alignment kernels | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
ncRNA type | Rfam Accession | N | ROC | SP | SN | nSV | ROC | SP | SN | nSV |
5S ribosomal RNA | RF00001 | 449 | 1.000 | 1.000 | 0.996 | 164.9 (1.3) | 1.000 | 1.000 | 0.996 | 4013.0 (31.1) |
U2 spliceosomal RNA | RF00004 | 566 | 0.999 | 1.000 | 0.993 | 631.2 (4.9) | 0.999 | 1.000 | 0.986 | 4117.5 (31.9) |
tRNA | RF00005 | 495 | 0.998 | 1.000 | 0.998 | 234.8 (1.8) | 1.000 | 1.000 | 0.998 | 4287.2 (33.2) |
Hammerhead ribozyme III | RF00008 | 588 | 1.000 | 1.000 | 0.997 | 221.2 (1.7) | 1.000 | 1.000 | 0.997 | 2452.1 (19.0) |
U3 snoRNA | RF00012 | 471 | 1.000 | 1.000 | 0.996 | 266.2 (2.1) | 0.998 | 1.000 | 0.870 | 4665.3 (36.2) |
U5 spliceosomal RNA | RF00020 | 510 | 1.000 | 1.000 | 0.996 | 525.5 (4.1) | 1.000 | 1.000 | 0.994 | 4060.0 (31.5) |
tmRNA | RF00023 | 730 | 1.000 | 1.000 | 0.997 | 685.8 (5.3) | 0.975 | 1.000 | 0.037 | 4677.7 (36.2) |
Group II intron | RF00029 | 604 | 1.000 | 1.000 | 0.993 | 482.7 (3.7) | 1.000 | 1.000 | 0.990 | 4217.3 (32.7) |
mir-10 | RF00104 | 620 | 1.000 | 1.000 | 0.998 | 59.5 (0.5) | 1.000 | 1.000 | 0.998 | 159.6 (1.2) |
U70 snoRNA | RF00156 | 608 | 0.999 | 1.000 | 0.990 | 195.0 (1.5) | 0.999 | 1.000 | 0.992 | 3811.8 (29.5) |
RNAse P | - | 656 | 1.000 | 1.000 | 0.991 | 490.6 (3.8) | 0.905 | 1.000 | 0.018 | 4729.2 (36.6) |
SRP RNA | - | 872 | 1.000 | 1.000 | 0.995 | 441.5 (3.4) | 0.908 | 1.000 | 0.900 | 4373.9 (33.9) |
Total | Â | 7169 | 1.000 | 1.000 | 0.995 | 4398.9 (2.9) | 0.977 | 1.000 | 0.788 | 45564.6 (29.5) |