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Table 3 Non-coding RNA detection using SVDD in comparing the stem kernels with the local alignment kernels.

From: Directed acyclic graph kernels for structural RNA analysis

    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)
  1. 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.