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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric ProbKnot RNAwolf
MCC 0.373 > 0.199
Average MCC ± 95% Confidence Intervals 0.398 ± 0.036 > 0.215 ± 0.027
Sensitivity 0.367 > 0.212
Positive Predictive Value 0.379 > 0.188
Total TP 7568 > 4369
Total TN 45325099 > 45321852
Total FP 17618 < 24745
Total FP CONTRA 2432 < 3879
Total FP INCONS 9975 < 14974
Total FP COMP 5211 < 5892
Total FN 13045 < 16244
P-value 3.56938820447e-08

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Performance plots


  1. Comparison of performance of ProbKnot 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 ProbKnot and RNAwolf).

  2. Comparison of average Matthews Correlation Coefficients (MCCs) for ProbKnot 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 ProbKnot and RNAwolf).

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Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP 7568
Total TN 45325099
Total FP 17618
Total FP CONTRA 2432
Total FP INCONS 9975
Total FP COMP 5211
Total FN 13045
Total Scores
MCC 0.373
Average MCC ± 95% Confidence Intervals 0.398 ± 0.036
Sensitivity 0.367
Positive Predictive Value 0.379
Nr of predictions 88

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00002 - 0.62 0.61 0.64 161 408807 138 15 77 46 103
CRW_00417 - 0.38 0.35 0.41 92 458176 145 22 113 10 170
CRW_00418 - 0.17 0.16 0.18 41 441105 195 17 167 11 219
CRW_00419 - 0.22 0.20 0.23 53 463939 184 19 155 10 212
CRW_00421 - 0.47 0.44 0.51 118 462970 138 19 96 23 148
CRW_00422 - 0.40 0.39 0.41 102 455284 172 23 126 23 161
CRW_00424 - 0.40 0.38 0.41 138 789063 222 20 175 27 225
CRW_00426 - 0.33 0.31 0.34 83 457203 172 20 140 12 182
CRW_00427 - 0.27 0.27 0.27 70 454324 205 34 153 18 191
CRW_00428 - 0.36 0.36 0.36 93 465837 182 33 132 17 167
CRW_00430 - 0.34 0.30 0.38 80 456282 139 29 99 11 186
CRW_00433 - 0.27 0.23 0.31 61 467830 144 12 125 7 202
CRW_00434 - 0.40 0.39 0.42 102 457205 147 21 118 8 161
CRW_00435 - 0.41 0.38 0.45 101 451501 135 17 106 12 164
CRW_00437 - 0.31 0.28 0.34 73 456277 152 21 119 12 187
CRW_00438 - 0.46 0.43 0.50 115 454349 130 20 97 13 153
CRW_00441 - 0.24 0.22 0.26 57 454362 173 22 140 11 205
CRW_00442 - 0.39 0.39 0.38 102 453363 175 42 121 12 159
CRW_00443 - 0.29 0.27 0.30 71 456253 185 27 139 19 189
CRW_00444 - 0.29 0.28 0.31 74 459121 179 26 140 13 189
CRW_00445 - 0.31 0.29 0.32 78 458162 170 32 131 7 187
CRW_00446 - 0.31 0.31 0.31 82 468730 198 29 155 14 183
CRW_00447 - 0.35 0.35 0.36 90 452428 179 23 135 21 170
CRW_00448 - 0.31 0.30 0.33 78 457209 178 24 135 19 183
CRW_00449 - 0.38 0.37 0.39 97 444850 160 29 120 11 163
CRW_00450 - 0.34 0.30 0.39 79 458199 141 17 108 16 183
CRW_00451 - 0.27 0.27 0.28 70 457197 195 30 149 16 194
CRW_00452 - 0.31 0.29 0.33 77 453394 184 26 131 27 185
CRW_00453 - 0.30 0.30 0.32 77 452432 174 31 136 7 184
CRW_00456 - 0.35 0.32 0.38 86 470708 157 22 119 16 179
CRW_00457 - 0.41 0.41 0.41 107 467768 172 31 122 19 157
CRW_00458 - 0.48 0.48 0.49 126 464874 149 26 104 19 138
CRW_00459 - 0.37 0.35 0.40 92 462012 157 22 115 20 171
CRW_00462 - 0.36 0.33 0.40 85 458191 137 23 104 10 176
CRW_00463 - 0.36 0.35 0.37 89 445797 171 31 123 17 165
CRW_00464 - 0.28 0.26 0.30 69 462009 170 17 146 7 195
CRW_00530 - 0.31 0.34 0.29 90 534781 233 62 162 9 178
CRW_00532 - 0.17 0.18 0.15 49 579103 287 75 199 13 216
CRW_00533 - 0.40 0.42 0.38 92 453389 204 31 116 57 127
CRW_00538 - 0.31 0.32 0.30 97 811851 252 60 167 25 203
CRW_00604 - 0.88 0.89 0.87 72 411695 196 2 9 185 9
CRW_00606 - 0.86 0.85 0.87 78 559063 257 2 10 245 14
CRW_00607 - 0.67 0.66 0.67 51 536054 291 10 15 266 26
CRW_00615 - 0.83 0.84 0.82 69 553794 281 5 10 266 13
CRW_00617 - 0.45 0.50 0.40 32 426346 256 12 36 208 32
CRW_00678 - 0.45 0.46 0.43 56 666306 280 17 56 207 65
CRW_00680 - 0.59 0.60 0.57 73 516509 238 11 43 184 49
CRW_00683 - 0.40 0.45 0.36 61 460150 213 35 74 104 74
CRW_00684 - 0.49 0.49 0.49 66 612037 256 19 49 188 69
CRW_00702 - 0.68 0.81 0.58 61 357329 217 33 12 172 14
CRW_00704 - 0.84 0.85 0.83 80 386664 204 7 9 188 14
CRW_00706 - 0.55 0.59 0.51 35 695541 358 15 19 324 24
CRW_00713 - 0.75 0.74 0.75 75 731345 330 6 19 305 26
CRW_00730 - 0.55 0.58 0.53 94 338897 161 19 66 76 67
CRW_00734 - 0.22 0.30 0.17 33 536969 252 96 68 88 77
CRW_00735 - 0.33 0.42 0.26 51 677834 301 68 77 156 70
CRW_00740 - 0.04 0.05 0.03 6 489370 304 70 109 125 107
CRW_00746 - 0.50 0.50 0.49 110 550501 193 24 90 79 109
CRW_00750 - 0.53 0.59 0.48 94 709642 281 30 70 181 66
CRW_00751 - 0.84 0.83 0.85 148 489380 166 4 23 139 30
CRW_00753 - 0.21 0.21 0.21 38 489372 233 35 110 88 140
CRW_00757 - 0.13 0.15 0.12 19 415258 251 40 99 112 107
CRW_00765 - 0.40 0.40 0.39 103 452412 172 38 123 11 154
CRW_00766 - 0.31 0.28 0.33 68 440187 154 23 113 18 172
CRW_00768 - 0.44 0.43 0.46 111 471666 155 19 110 26 148
CRW_00769 - 0.54 0.53 0.56 134 451485 127 28 78 21 118
CRW_00773 - 0.53 0.53 0.54 136 451474 132 27 88 17 123
CRW_00774 - 0.36 0.35 0.38 91 488326 168 24 125 19 172
CRW_00777 - 0.38 0.39 0.38 118 719086 236 39 157 40 186
CRW_00780 - 0.26 0.23 0.30 58 475606 150 17 119 14 197
CRW_00783 - 0.28 0.27 0.30 71 453388 180 22 147 11 188
CRW_00784 - 0.25 0.24 0.27 63 456254 187 31 142 14 199
CRW_00785 - 0.27 0.26 0.28 66 452441 182 20 149 13 187
CRW_00787 - 0.44 0.42 0.46 129 646674 179 14 136 29 177
CRW_00794 - 0.28 0.28 0.28 68 434537 200 16 157 27 178
CRW_00796 - 0.30 0.29 0.32 67 384793 164 13 130 21 168
CRW_00797 - 0.38 0.38 0.38 131 692904 250 35 183 32 211
CRW_00801 - 0.42 0.42 0.41 105 438262 167 37 112 18 144
CRW_00802 - 0.20 0.19 0.21 48 460092 200 26 154 20 205
CRW_00813 - 0.31 0.35 0.27 47 530793 264 47 78 139 86
CRW_01186 - 0.29 0.28 0.29 109 836194 279 38 230 11 277
CRW_01250 - 0.35 0.34 0.36 127 781522 241 33 193 15 251
CRW_01266 - 0.26 0.26 0.26 100 818174 298 49 237 12 281
CRW_01271 - 0.35 0.35 0.35 134 827163 253 42 202 9 247
CRW_01344 - 0.29 0.28 0.30 103 791562 258 40 206 12 263
PDB_00409 - 0.31 0.37 0.27 91 688208 326 81 171 74 154
PDB_00805 - 0.61 0.59 0.64 177 467751 133 13 87 33 125
PDB_01261 - 0.71 0.64 0.78 214 467754 64 0 60 4 122

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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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