Table 2.
Using the structural alignments of 63 eukaryotic SRP RNAs [32], and 51 eukaryotic nuclear RNaseP RNAs [33] we generated a total of 3342 pairwise structural RNA alignments that we scored with QRNA. Here we present the sensitivity and specificity of our method in identifying those alignments as RNAs with a posterior log-odds score > 5 bits. Specificity was estimated by shuffling the alignments by columns, such that the percentage identity remains intact, but the structure is removed. Results are broken down with respect to the percentage identity, and also with respect to the GC content of the alignments.
| # align | % sensitivity | % specificity | |
| % ID | |||
| 0 < 10 | 140 | 42.8 (60) | 100.0 (0) |
| 10 < 20 | 827 | 59.6 (493) | 100.0 (0) |
| 20 < 30 | 503 | 71.4 (359) | 100.0 (0) |
| 30 < 40 | 764 | 75.1 (574) | 100.0 (0) |
| 40 < 50 | 283 | 58.6 (166) | 100.0 (0) |
| 50 < 60 | 434 | 81.3 (353) | 100.0 (0) |
| 60 < 70 | 88 | 80.7 (71) | 100.0 (0) |
| 70 < 80 | 70 | 91.4 (64) | 97.1 (2) |
| 80 < 90 | 73 | 97.3 (71) | 79.4 (15) |
| 90 < 100 | 61 | 93.4 (57) | 27.9 (44) |
| 100 | 99 | 93.9 (93) | 29.3 (70) |
| % GC | |||
| 35 < 40 | 31 | 51.6 (16) | 93.5 (2) |
| 40 < 45 | 343 | 69.1 (237) | 96.5 (12) |
| 45 < 50 | 1131 | 72.4 (819) | 97.9 (24) |
| 50 < 55 | 1320 | 69.2 (914) | 96.5 (46) |
| 55 < 60 | 508 | 73.0 (371) | 91.3 (44) |
| 60 < 65 | 9 | 44.4 (4) | 66.7 (3) |