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Table of contents:

  1. Overview

  2. Performance Plots

  3. Performance of IPknot - scored higher in this pairwise comparison

  4. Performance of RNAwolf - scored lower in this pairwise comparison

  5. Compile and download dataset for IPknot & RNAwolf [.zip] - may take several seconds...


Overview

Metric IPknot RNAwolf
MCC 0.441 > 0.199
Average MCC ± 95% Confidence Intervals 0.466 ± 0.036 > 0.215 ± 0.027
Sensitivity 0.354 > 0.212
Positive Predictive Value 0.550 > 0.188
Total TP 7289 > 4369
Total TN 45331829 > 45321852
Total FP 9487 < 24745
Total FP CONTRA 1117 < 3879
Total FP INCONS 4839 < 14974
Total FP COMP 3531 < 5892
Total FN 13324 < 16244
P-value 3.56938820447e-08

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Performance plots


  1. Comparison of performance of IPknot and RNAwolf. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for IPknot and RNAwolf).

  2. Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot and RNAwolf. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for IPknot and RNAwolf).

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Performance of IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP 7289
Total TN 45331829
Total FP 9487
Total FP CONTRA 1117
Total FP INCONS 4839
Total FP COMP 3531
Total FN 13324
Total Scores
MCC 0.441
Average MCC ± 95% Confidence Intervals 0.466 ± 0.036
Sensitivity 0.354
Positive Predictive Value 0.550
Nr of predictions 88

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2. Individual counts for IPknot [ download as .csv ]

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00002 - 0.64 0.53 0.77 139 408879 64 18 24 22 125
CRW_00417 - 0.43 0.36 0.52 95 458219 97 18 71 8 167
CRW_00418 - 0.34 0.23 0.50 60 441209 66 5 56 5 200
CRW_00419 - 0.38 0.28 0.52 73 464026 72 7 60 5 192
CRW_00421 - 0.53 0.39 0.72 103 463060 53 4 36 13 163
CRW_00422 - 0.48 0.37 0.64 96 455385 74 8 46 20 167
CRW_00424 - 0.42 0.32 0.55 117 789184 104 10 85 9 246
CRW_00426 - 0.34 0.28 0.41 75 457262 117 15 94 8 190
CRW_00427 - 0.29 0.25 0.35 64 454397 126 20 100 6 197
CRW_00428 - 0.48 0.37 0.64 95 465946 65 11 43 11 165
CRW_00430 - 0.38 0.27 0.55 71 456361 67 8 50 9 195
CRW_00433 - 0.35 0.24 0.53 63 467908 59 3 54 2 200
CRW_00434 - 0.41 0.29 0.57 77 457310 60 10 49 1 186
CRW_00435 - 0.35 0.26 0.48 68 451584 77 6 67 4 197
CRW_00437 - 0.32 0.24 0.42 62 456344 92 9 75 8 198
CRW_00438 - 0.44 0.34 0.56 92 454416 83 8 65 10 176
CRW_00441 - 0.30 0.20 0.44 52 454463 69 13 53 3 210
CRW_00442 - 0.40 0.31 0.52 81 453471 81 13 63 5 180
CRW_00443 - 0.33 0.23 0.46 61 456358 81 9 62 10 199
CRW_00444 - 0.43 0.30 0.60 80 459228 59 5 48 6 183
CRW_00445 - 0.36 0.28 0.46 74 458242 92 11 76 5 191
CRW_00446 - 0.40 0.34 0.47 90 468803 112 14 89 9 175
CRW_00447 - 0.36 0.28 0.47 73 452521 91 10 72 9 187
CRW_00448 - 0.44 0.30 0.67 77 457331 46 7 31 8 184
CRW_00449 - 0.34 0.23 0.49 61 444971 65 6 58 1 199
CRW_00450 - 0.33 0.24 0.45 62 458265 89 11 65 13 200
CRW_00451 - 0.39 0.31 0.49 81 457279 94 10 76 8 183
CRW_00452 - 0.39 0.29 0.54 75 453490 77 8 55 14 187
CRW_00453 - 0.37 0.27 0.51 70 452540 75 7 59 9 191
CRW_00456 - 0.44 0.31 0.61 83 470798 60 10 44 6 182
CRW_00457 - 0.51 0.42 0.61 111 467846 86 13 58 15 153
CRW_00458 - 0.53 0.42 0.67 112 464963 60 6 49 5 152
CRW_00459 - 0.58 0.44 0.76 115 462090 50 5 31 14 148
CRW_00462 - 0.41 0.29 0.58 76 458271 66 6 50 10 185
CRW_00463 - 0.43 0.36 0.51 92 445860 95 22 66 7 162
CRW_00464 - 0.49 0.30 0.81 78 462145 24 1 17 6 186
CRW_00530 - 0.34 0.26 0.45 71 534937 94 30 57 7 197
CRW_00532 - 0.24 0.17 0.33 46 579285 103 22 73 8 219
CRW_00533 - 0.50 0.42 0.59 91 453474 81 19 44 18 128
CRW_00538 - 0.34 0.25 0.46 76 812010 109 15 74 20 224
CRW_00604 - 0.89 0.86 0.91 70 411701 129 5 2 122 11
CRW_00606 - 0.89 0.85 0.94 78 559070 188 0 5 183 14
CRW_00607 - 0.76 0.73 0.80 56 536060 259 10 4 245 21
CRW_00615 - 0.86 0.77 0.95 63 553812 211 0 3 208 19
CRW_00617 - 0.48 0.45 0.52 29 426370 178 4 23 151 35
CRW_00678 - 0.59 0.58 0.60 70 666319 212 9 37 166 51
CRW_00680 - 0.68 0.69 0.67 84 516510 190 13 29 148 38
CRW_00683 - 0.65 0.62 0.69 84 460198 151 11 27 113 51
CRW_00684 - 0.58 0.53 0.63 72 612057 178 14 28 136 63
CRW_00702 - 0.86 0.83 0.89 62 357365 141 7 1 133 13
CRW_00704 - 0.91 0.90 0.92 85 386668 146 4 3 139 9
CRW_00706 - 0.64 0.69 0.59 41 695540 219 11 18 190 18
CRW_00713 - 0.84 0.76 0.93 77 731362 240 1 5 234 24
CRW_00730 - 0.46 0.45 0.46 73 338918 141 20 65 56 88
CRW_00734 - 0.62 0.48 0.80 53 537100 84 2 11 71 57
CRW_00735 - 0.54 0.49 0.60 59 677931 126 11 29 86 62
CRW_00740 - 0.02 0.03 0.02 3 489422 159 62 68 29 110
CRW_00746 - 0.64 0.59 0.70 129 550542 110 18 36 56 90
CRW_00750 - 0.58 0.57 0.60 91 709684 186 19 42 125 69
CRW_00751 - 0.80 0.74 0.86 132 489402 79 12 9 58 46
CRW_00753 - 0.17 0.15 0.20 27 489421 156 27 80 49 151
CRW_00757 - 0.14 0.13 0.14 17 415291 164 36 72 56 109
CRW_00765 - 0.46 0.37 0.57 96 452509 76 13 58 5 161
CRW_00766 - 0.32 0.24 0.44 57 440262 83 10 62 11 183
CRW_00768 - 0.59 0.47 0.73 122 471740 54 6 38 10 137
CRW_00769 - 0.56 0.46 0.66 117 451549 68 12 47 9 135
CRW_00773 - 0.42 0.37 0.48 95 451526 109 19 85 5 164
CRW_00774 - 0.50 0.35 0.72 93 488436 52 4 33 15 170
CRW_00777 - 0.40 0.34 0.47 102 719185 131 23 90 18 202
CRW_00780 - 0.29 0.21 0.39 54 475662 88 18 66 4 201
CRW_00783 - 0.32 0.22 0.45 58 453499 79 9 62 8 201
CRW_00784 - 0.34 0.27 0.43 70 456326 105 18 76 11 192
CRW_00785 - 0.46 0.34 0.61 86 452536 58 8 46 4 167
CRW_00787 - 0.39 0.32 0.49 97 646753 108 19 84 5 209
CRW_00794 - 0.37 0.28 0.49 68 434640 81 10 60 11 178
CRW_00796 - 0.28 0.19 0.43 44 384901 70 6 52 12 191
CRW_00797 - 0.37 0.28 0.49 97 693054 121 12 90 19 245
CRW_00801 - 0.44 0.39 0.49 96 438322 108 21 77 10 153
CRW_00802 - 0.41 0.32 0.52 82 460161 86 14 63 9 171
CRW_00813 - 0.47 0.44 0.49 59 530845 179 12 49 118 74
CRW_01186 - 0.43 0.34 0.55 133 836328 116 15 95 6 253
CRW_01250 - 0.39 0.33 0.47 123 781612 152 20 120 12 255
CRW_01266 - 0.42 0.36 0.50 136 818290 147 12 122 13 245
CRW_01271 - 0.48 0.40 0.56 153 827269 128 20 99 9 228
CRW_01344 - 0.38 0.30 0.47 110 791679 131 20 102 9 256
PDB_00409 - 0.33 0.37 0.30 91 688246 288 61 153 74 154
PDB_00805 - 0.68 0.57 0.81 172 467816 53 6 34 13 130
PDB_01261 - 0.68 0.55 0.84 185 467809 34 0 34 0 151

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Performance of RNAwolf - scored lower in this pairwise comparison

1. Total counts & total scores for RNAwolf

Total Base Pair Counts
Total TP 4369
Total TN 45321852
Total FP 24745
Total FP CONTRA 3879
Total FP INCONS 14974
Total FP COMP 5892
Total FN 16244
Total Scores
MCC 0.199
Average MCC ± 95% Confidence Intervals 0.215 ± 0.027
Sensitivity 0.212
Positive Predictive Value 0.188
Nr of predictions 88

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2. Individual counts for RNAwolf [ download as .csv ]

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00002 - 0.28 0.29 0.27 76 408775 248 40 169 39 188
CRW_00417 - 0.16 0.16 0.15 43 458123 262 39 198 25 219
CRW_00418 - 0.14 0.15 0.14 38 441051 257 48 193 16 222
CRW_00419 - 0.13 0.14 0.12 36 463875 271 46 209 16 229
CRW_00421 - 0.17 0.18 0.16 48 462897 276 52 206 18 218
CRW_00422 - 0.15 0.16 0.14 41 455242 274 39 213 22 222
CRW_00424 - 0.20 0.21 0.19 75 789009 339 43 269 27 288
CRW_00426 - 0.22 0.23 0.22 60 457173 236 41 172 23 205
CRW_00427 - 0.26 0.26 0.26 69 454312 242 35 165 42 192
CRW_00428 - 0.17 0.18 0.16 48 465797 277 52 198 27 212
CRW_00430 - 0.10 0.11 0.10 29 456197 279 45 219 15 237
CRW_00433 - 0.20 0.20 0.19 53 467752 243 36 187 20 210
CRW_00434 - 0.14 0.15 0.14 39 457167 272 43 197 32 224
CRW_00435 - 0.17 0.17 0.17 45 451453 253 34 193 26 220
CRW_00437 - 0.26 0.27 0.26 69 456226 230 32 163 35 191
CRW_00438 - 0.16 0.16 0.15 44 454297 253 44 196 13 224
CRW_00441 - 0.14 0.15 0.14 38 454303 253 49 191 13 224
CRW_00442 - 0.15 0.15 0.14 39 453356 254 41 192 21 222
CRW_00443 - 0.20 0.20 0.20 52 456224 251 42 172 37 208
CRW_00444 - 0.23 0.24 0.23 62 459095 240 39 165 36 201
CRW_00445 - 0.23 0.25 0.22 65 458114 258 46 178 34 200
CRW_00446 - 0.11 0.11 0.10 30 468710 276 47 209 20 235
CRW_00447 - 0.14 0.15 0.13 38 452387 274 38 213 23 222
CRW_00448 - 0.08 0.08 0.08 22 457185 260 47 192 21 239
CRW_00449 - 0.09 0.10 0.09 25 444821 265 45 205 15 235
CRW_00450 - 0.17 0.18 0.16 46 458120 263 37 200 26 216
CRW_00451 - 0.18 0.19 0.18 51 457155 266 47 193 26 213
CRW_00452 - 0.14 0.15 0.13 39 453337 275 42 210 23 223
CRW_00453 - 0.25 0.25 0.25 64 452419 227 33 160 34 197
CRW_00456 - 0.19 0.19 0.19 50 470672 235 38 175 22 215
CRW_00457 - 0.27 0.28 0.27 75 467746 248 26 181 41 189
CRW_00458 - 0.27 0.27 0.27 71 464866 208 41 152 15 193
CRW_00459 - 0.22 0.23 0.22 60 461968 248 35 178 35 203
CRW_00462 - 0.19 0.20 0.18 51 458126 254 29 197 28 210
CRW_00463 - 0.21 0.22 0.20 56 445761 243 47 176 20 198
CRW_00464 - 0.17 0.17 0.17 44 461979 238 40 178 20 220
CRW_00530 - 0.24 0.27 0.22 72 534761 278 73 189 16 196
CRW_00532 - 0.18 0.20 0.16 54 579094 303 69 209 25 211
CRW_00533 - 0.28 0.31 0.26 67 453372 266 43 146 77 152
CRW_00538 - 0.21 0.24 0.18 72 811777 358 86 240 32 228
CRW_00604 - 0.81 0.81 0.80 66 411696 242 2 14 226 15
CRW_00606 - 0.72 0.73 0.72 67 559060 311 5 21 285 25
CRW_00607 - 0.45 0.45 0.44 35 536050 325 12 33 280 42
CRW_00615 - 0.44 0.55 0.36 45 553753 334 38 42 254 37
CRW_00617 - 0.07 0.09 0.05 6 426305 316 43 72 201 58
CRW_00678 - 0.16 0.18 0.14 22 666279 384 32 102 250 99
CRW_00680 - 0.25 0.28 0.23 34 516487 293 22 93 178 88
CRW_00683 - 0.10 0.13 0.09 17 460126 313 48 129 136 118
CRW_00684 - 0.10 0.13 0.09 17 611976 357 48 130 179 118
CRW_00702 - 0.30 0.35 0.25 26 357333 263 32 44 187 49
CRW_00704 - 0.33 0.36 0.31 34 386650 255 25 51 179 60
CRW_00706 - 0.43 0.46 0.40 27 695542 380 10 31 339 32
CRW_00713 - 0.38 0.41 0.35 41 731327 351 24 53 274 60
CRW_00730 - 0.42 0.46 0.39 74 338884 207 22 96 89 87
CRW_00734 - 0.19 0.25 0.14 28 536966 318 85 87 146 82
CRW_00735 - 0.18 0.23 0.13 28 677820 354 81 101 172 93
CRW_00740 - 0.03 0.04 0.02 5 489307 321 131 112 78 108
CRW_00746 - 0.22 0.24 0.19 53 550453 297 42 177 78 166
CRW_00750 - 0.12 0.12 0.12 19 709674 362 28 115 219 141
CRW_00751 - 0.51 0.54 0.48 96 489353 226 22 84 120 82
CRW_00753 - 0.09 0.10 0.08 18 489326 306 44 167 95 160
CRW_00757 - 0.12 0.15 0.10 19 415231 297 55 111 131 107
CRW_00765 - 0.13 0.14 0.12 37 452376 272 55 208 9 220
CRW_00766 - 0.14 0.15 0.13 35 440129 259 41 186 32 205
CRW_00768 - 0.30 0.32 0.29 83 471617 239 48 158 33 176
CRW_00769 - 0.21 0.23 0.20 58 451429 261 51 187 23 194
CRW_00773 - 0.32 0.33 0.31 85 451453 218 45 142 31 174
CRW_00774 - 0.15 0.16 0.14 42 488276 276 32 216 28 221
CRW_00777 - 0.09 0.10 0.08 31 719031 376 64 274 38 273
CRW_00780 - 0.19 0.20 0.18 50 475527 242 42 181 19 205
CRW_00783 - 0.13 0.14 0.12 35 453340 266 49 204 13 224
CRW_00784 - 0.17 0.18 0.16 48 456191 277 37 214 26 214
CRW_00785 - 0.21 0.22 0.21 55 452412 242 43 166 33 198
CRW_00787 - 0.18 0.19 0.18 59 646617 305 35 242 28 247
CRW_00794 - 0.13 0.15 0.12 36 434484 283 53 205 25 210
CRW_00796 - 0.05 0.06 0.05 14 384732 272 52 205 15 221
CRW_00797 - 0.13 0.14 0.12 47 692868 356 57 281 18 295
CRW_00801 - 0.18 0.19 0.17 48 438233 249 59 176 14 201
CRW_00802 - 0.12 0.13 0.11 33 460031 275 47 209 19 220
CRW_00813 - 0.11 0.15 0.08 20 530728 326 95 122 109 113
CRW_01186 - 0.19 0.19 0.18 75 836163 348 55 278 15 311
CRW_01250 - 0.22 0.22 0.22 85 781486 328 41 263 24 293
CRW_01266 - 0.19 0.20 0.18 76 818139 366 54 291 21 305
CRW_01271 - 0.17 0.17 0.17 65 827149 364 36 291 37 316
CRW_01344 - 0.16 0.16 0.16 59 791531 333 54 267 12 307
PDB_00409 - 0.29 0.34 0.24 84 688207 347 81 179 87 161
PDB_00805 - 0.34 0.36 0.33 108 467696 243 40 184 19 194
PDB_01261 - 0.52 0.50 0.54 168 467715 157 13 132 12 168

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Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.

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