Table 1 Quality of non-canonical base pair prediction for RNA STRAND-deposited structures (best values in bold)
From: New in silico approach to assessing RNA secondary structures with non-canonical base pairs
| Â | Sequence length (nts) | ||||
|---|---|---|---|---|---|
1–50 | 51–100 | 101–200 | 201–500 | ||
Number of reference structures that include non-canonical base pairs | 319 | 126 | 188 | 455 | |
Total number of non-canonical base pairs observed in reference structures | 641 | 300 | 607 | 2252 | |
(a) Results for non-canonical base pairs predicted from sequence | |||||
Number (and percentage) of correctly predicted non-canonical base pairs present in the reference structures | RNAwolf | 171 (26.68) | 38 (12.67) | 44 (7.25) | 149 (6.62) |
MC-Fold-DP | 405 (63.18) | 94 (31.33) | 157 (25.86) | 636 (28.24) | |
MC-Fold | 363 (56.63) | 82 (27.33) | 167 (27.51) | n/a | |
RC/Rp-1 | 369 (57.57) | 111 (37.00) | 291 (47.94) | 690 (30.64) | |
RC/Rp-2 | 311 (48.52) | 79 (26.33) | 244 (40.20) | 618 (27.44) | |
RC/Rp-3 | 312 (48.67) | 81 (27.00) | 225 (37.07) | 654 (29.04) | |
Total number of predicted non-canonical base pairs | RNAwolf | 893 | 501 | 1334 | 8616 |
MC-Fold-DP | 1099 | 1040 | 2891 | 20123 | |
MC-Fold | 816 | 699 | 1825 | n/a | |
RC/Rp-1 | 1493 | 1462 | 4453 | 26050 | |
RC/Rp-2 | 1418 | 1235 | 4041 | 27282 | |
RC/Rp-3 | 949 | 698 | 2968 | 14756 | |
(b) Results for non-canonical base pairs predicted from canonical secondary structure | |||||
Number (and percentage) of correctly predicted non-canonical base pairs present in the reference structures | RNAwolf | 214 (33.39) | 67 (22.33) | 268 (44.15) | 772 (34.28) |
MC-Fold-DP | n/a | n/a | n/a | n/a | |
MC-Fold | 334 (52.11) | 136 (45.33) | 279 (45.96) | n/a | |
RC/Rp-1 | 452 (70.51) | 173 (57.67) | 337 (55.52) | 1124 (49.91) | |
RC/Rp-2 | 398 (62.09) | 131 (43.67) | 290 (47.78) | 974 (43.25) | |
RC/Rp-3 | 408 (63.65) | 145 (48.33) | 261 (43.00) | 1051 (46.67) | |
Total number of predicted non-canonical base pairs | RNAwolf | 352 | 154 | 461 | 2183 |
MC-Fold-DP | n/a | n/a | n/a | n/a | |
MC-Fold | 335 | 137 | 279 | n/a | |
RC/Rp-1 | 1404 | 1470 | 4145 | 26479 | |
RC/Rp-2 | 1273 | 1191 | 3978 | 26287 | |
RC/Rp-3 | 969 | 672 | 2754 | 15011 | |