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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

    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   7169 1.000 1.000 0.995 4398.9 (2.9) 0.977 1.000 0.788 45564.6 (29.5)
  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.