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. 2005 Jan 21;102(7):2454–2459. doi: 10.1073/pnas.0409169102

Table 1. Detection performance for different classes of ncRNAs.

Cutoff, classification probability
0.5
0.9
0.99
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.