Table 1. Detection performance for different classes of ncRNAs.
Cutoff, classification probability
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0.5
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0.9
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0.99
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ncRNA type | N | Sensitivity | Specificity | Sensitivity | Specificity | Sensitivity | Specificity |
5S ribosomal RNA | 297 | 81.48 (242) | 96.63 (10) | 68.69 (204) | 99.33 (2) | 33.00 (98) | 100.00 (0) |
tRNA | 329 | 94.83 (312) | 93.62 (21) | 90.27 (297) | 97.87 (7) | 75.68 (249) | 99.70 (1) |
SRP RNA | 464 | 100.00 (464) | 96.55 (16) | 96.55 (448) | 98.92 (5) | 66.16 (307) | 100.00 (0) |
RNAse P | 291 | 98.97 (288) | 96.22 (11) | 84.19 (245) | 99.31 (2) | 56.70 (165) | 100.00 (0) |
U2 spliceosomal RNA | 351 | 98.58 (346) | 97.72 (8) | 95.44 (335) | 99.15 (3) | 66.67 (234) | 99.72 (1) |
U5 spliceosomal RNA | 285 | 91.58 (261) | 98.25 (5) | 81.75 (233) | 100.00 (0) | 70.53 (201) | 100.00 (0) |
U3 snoRNA | 277 | 83.75 (232) | 98.56 (4) | 62.82 (174) | 99.28 (2) | 44.40 (123) | 99.64 (1) |
U70 snoRNA | 363 | 61.16 (222) | 96.69 (12) | 35.54 (129) | 98.90 (4) | 17.91 (65) | 99.72 (1) |
Hammerhead III ribozyme | 271 | 100.00 (271) | 95.20 (13) | 98.15 (266) | 98.89 (3) | 89.67 (243) | 99.26 (2) |
Group II catalytic intron | 407 | 78.62 (320) | 96.31 (15) | 76.90 (313) | 98.53 (6) | 25.31 (103) | 100.00 (0) |
tmRNA | 386 | 24.87 (96) | 96.37 (14) | 18.65 (72) | 98.19 (7) | 8.55 (33) | 99.48 (2) |
MicroRNA mir-10 | 380 | 100.00 (380) | 95.26 (18) | 97.63 (371) | 99.21 (3) | 62.37 (237) | 100.00 (0) |
Total | 4,101 | 84.17 (3,452) | 96.42 (147) | 75.27 (3,087) | 98.93 (44) | 50.18 (2,058) | 99.80 (8) |
Results for alignments with two to four sequences and mean pairwise identities between 60% and 100% are shown. N is the number of alignments in the test set. For each native alignment, one randomized alignment was produced, and randomized alignments classified as ncRNA were counted as false positives. Sensitivity and specificity are shown in percentage for three cutoffs of the RNA class probability predicted by the SVM. Absolute numbers of true positives and false negatives are shown in parentheses.