Table 3.
Non-coding RNA detection using SVDD in comparing the stem kernels with the local alignment kernels.
| 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 | 0.940 | 27.8 (6.9) | 1.000 | 1.000 | 0.886 | 48.4 (12.0) |
| U2 spliceosomal RNA | RF00004 | 566 | 0.997 | 0.999 | 0.912 | 51.8 (10.2) | 0.999 | 1.000 | 0.844 | 92.0 (18.1) |
| tRNA | RF00005 | 495 | 0.983 | 0.948 | 0.939 | 26.8 (6.0) | 0.999 | 0.999 | 0.853 | 67.0 (15.0) |
| Hammerhead ribozyme III | RF00008 | 588 | 1.000 | 0.998 | 0.971 | 14.2 (2.7) | 1.000 | 1.000 | 0.968 | 19.3 (3.6) |
| U3 snoRNA | RF00012 | 471 | 1.000 | 1.000 | 0.915 | 36.3 (8.6) | 0.959 | 1.000 | 0.775 | 95.5 (22.5) |
| U5 spliceosomal RNA | RF00020 | 510 | 0.999 | 0.998 | 0.939 | 30.3 (6.6) | 1.000 | 1.000 | 0.882 | 57.2 (12.5) |
| tmRNA | RF00023 | 730 | 1.000 | 1.000 | 0.881 | 83.1 (12.6) | 0.757 | 1.000 | 0.037 | 636.5 (96.9) |
| Group II intron | RF00029 | 604 | 0.996 | 0.989 | 0.942 | 30.9 (5.7) | 0.999 | 1.000 | 0.922 | 48.7 (9.0) |
| mir-10 | RF00104 | 620 | 1.000 | 1.000 | 0.977 | 13.3 (2.4) | 1.000 | 1.000 | 0.984 | 10.7 (1.9) |
| U70 snoRNA | RF00156 | 608 | 0.998 | 0.996 | 0.952 | 25.5 (4.7) | 1.000 | 1.000 | 0.951 | 29.0 (5.3) |
| RNAse P | - | 656 | 0.998 | 1.000 | 0.887 | 66.2 (11.2) | 0.629 | 1.000 | 0.006 | 587.5 (99.5) |
| SRP RNA | - | 872 | 1.000 | 1.000 | 0.939 | 54.4 (6.9) | 0.994 | 1.000 | 0.881 | 95.3 (12.1) |
| Total | 7169 | 0.998 | 0.995 | 0.932 | 460.6 (7.1) | 0.938 | 1.000 | 0.729 | 1787.1 (27.7) | |
ncRNA type: name of the target ncRNA family. Rfam Accession: accession number of the target ncRNA family in Rfam. N: number of alignments. ROC: ROC score, equal to the area under the ROC curve. SP: specificity of the discrimination of the target ncRNA family. SN: sensitivity of the discrimination of the target ncRNA family. nSV: number of support vectors collected in the training processes and their rates against the numbers of the training alignments within parentheses.