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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

  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