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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric CentroidFold RNAwolf
MCC 0.436 > 0.198
Average MCC ± 95% Confidence Intervals 0.466 ± 0.037 > 0.215 ± 0.029
Sensitivity 0.350 > 0.208
Positive Predictive Value 0.545 > 0.188
Total TP 6559 > 3908
Total TN 39601063 > 39592372
Total FP 8686 < 21488
Total FP CONTRA 850 < 3257
Total FP INCONS 4634 < 13569
Total FP COMP 3202 < 4662
Total FN 12204 < 14855
P-value 3.56938820447e-08

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Performance plots


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

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

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Performance of CentroidFold - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidFold

Total Base Pair Counts
Total TP 6559
Total TN 39601063
Total FP 8686
Total FP CONTRA 850
Total FP INCONS 4634
Total FP COMP 3202
Total FN 12204
Total Scores
MCC 0.436
Average MCC ± 95% Confidence Intervals 0.466 ± 0.037
Sensitivity 0.350
Positive Predictive Value 0.545
Nr of predictions 77

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00002 - 0.61 0.42 0.87 112 408931 51 0 17 34 152
CRW_00417 - 0.43 0.33 0.55 86 458248 77 14 55 8 176
CRW_00418 - 0.26 0.19 0.36 49 441193 89 7 81 1 211
CRW_00419 - 0.36 0.27 0.47 71 464016 84 5 74 5 194
CRW_00421 - 0.51 0.42 0.63 111 463028 80 7 57 16 155
CRW_00422 - 0.41 0.33 0.52 87 455367 99 11 70 18 176
CRW_00424 - 0.48 0.40 0.58 145 789146 122 5 100 17 218
CRW_00426 - 0.43 0.35 0.53 94 457268 91 7 77 7 171
CRW_00427 - 0.28 0.23 0.33 61 454396 136 25 99 12 200
CRW_00428 - 0.43 0.33 0.55 87 465937 79 14 57 8 173
CRW_00430 - 0.36 0.26 0.50 70 456351 73 13 56 4 196
CRW_00433 - 0.31 0.21 0.44 56 467902 74 4 66 4 207
CRW_00434 - 0.50 0.37 0.67 97 457301 54 8 40 6 166
CRW_00435 - 0.32 0.22 0.46 59 451596 77 8 62 7 206
CRW_00437 - 0.26 0.20 0.33 53 456331 112 13 93 6 207
CRW_00438 - 0.32 0.25 0.41 68 454416 105 12 85 8 200
CRW_00441 - 0.37 0.27 0.53 70 454448 67 6 57 4 192
CRW_00442 - 0.34 0.25 0.45 66 453480 92 8 74 10 195
CRW_00443 - 0.31 0.21 0.45 55 456367 78 4 64 10 205
CRW_00444 - 0.44 0.32 0.61 85 459222 61 10 44 7 178
CRW_00445 - 0.45 0.37 0.55 99 458224 87 12 68 7 166
CRW_00446 - 0.34 0.29 0.41 77 468807 124 14 98 12 188
CRW_00447 - 0.30 0.25 0.35 66 452488 131 16 106 9 194
CRW_00448 - 0.28 0.21 0.38 55 457300 97 18 73 6 206
CRW_00449 - 0.43 0.31 0.59 80 444961 60 11 44 5 180
CRW_00450 - 0.41 0.27 0.62 72 458286 58 4 41 13 190
CRW_00451 - 0.39 0.28 0.53 75 457305 72 6 60 6 189
CRW_00452 - 0.46 0.33 0.65 86 453495 63 5 42 16 176
CRW_00453 - 0.35 0.25 0.47 66 452537 84 5 68 11 195
CRW_00456 - 0.43 0.29 0.64 78 470813 48 5 39 4 187
CRW_00457 - 0.48 0.38 0.59 101 467857 82 10 60 12 163
CRW_00458 - 0.45 0.34 0.61 89 464984 66 3 54 9 175
CRW_00459 - 0.50 0.41 0.61 109 462061 91 8 63 20 154
CRW_00462 - 0.44 0.31 0.60 82 458267 67 4 50 13 179
CRW_00463 - 0.45 0.37 0.54 94 445867 85 17 62 6 160
CRW_00464 - 0.47 0.33 0.68 87 462113 50 4 37 9 177
CRW_00530 - 0.37 0.31 0.44 84 534904 119 34 73 12 184
CRW_00538 - 0.40 0.30 0.54 90 812009 98 11 65 22 210
CRW_00604 - 0.86 0.84 0.88 68 411701 143 3 6 134 13
CRW_00606 - 0.94 0.90 0.99 83 559069 184 0 1 183 9
CRW_00607 - 0.85 0.75 0.95 58 536069 241 0 3 238 19
CRW_00615 - 0.90 0.83 0.97 68 553808 240 0 2 238 14
CRW_00617 - 0.53 0.48 0.58 31 426373 170 6 16 148 33
CRW_00678 - 0.46 0.44 0.48 53 666324 233 11 47 175 68
CRW_00680 - 0.55 0.54 0.56 66 516518 178 13 39 126 56
CRW_00683 - 0.63 0.59 0.67 79 460202 174 2 37 135 56
CRW_00684 - 0.53 0.50 0.56 68 612050 219 16 37 166 67
CRW_00702 - 0.76 0.73 0.80 55 357366 141 5 9 127 20
CRW_00704 - 0.89 0.87 0.91 82 386670 176 3 5 168 12
CRW_00706 - 0.69 0.71 0.68 42 695548 245 8 12 225 17
CRW_00713 - 0.82 0.72 0.94 73 731367 238 1 4 233 28
CRW_00765 - 0.41 0.33 0.51 85 452509 86 16 66 4 172
CRW_00766 - 0.27 0.20 0.39 47 440269 88 14 61 13 193
CRW_00768 - 0.63 0.49 0.81 128 471747 57 6 25 26 131
CRW_00769 - 0.50 0.39 0.64 99 451570 74 13 43 18 153
CRW_00773 - 0.50 0.42 0.60 108 451545 87 15 57 15 151
CRW_00774 - 0.50 0.39 0.63 103 488403 77 3 57 17 160
CRW_00777 - 0.35 0.27 0.44 83 719210 137 18 89 30 221
CRW_00780 - 0.34 0.28 0.42 71 475629 114 18 82 14 184
CRW_00783 - 0.40 0.29 0.55 75 453491 73 7 55 11 184
CRW_00784 - 0.42 0.33 0.54 87 456330 83 15 58 10 175
CRW_00785 - 0.52 0.39 0.70 99 452535 48 8 34 6 154
CRW_00787 - 0.50 0.40 0.63 123 646759 83 6 65 12 183
CRW_00794 - 0.36 0.29 0.44 72 434613 106 13 80 13 174
CRW_00796 - 0.36 0.23 0.57 55 384906 60 0 42 18 180
CRW_00797 - 0.35 0.27 0.44 94 693037 141 20 102 19 248
CRW_00801 - 0.45 0.38 0.53 94 438339 92 22 61 9 155
CRW_00802 - 0.37 0.30 0.46 76 460153 109 16 75 18 177
CRW_00813 - 0.45 0.42 0.48 56 530849 163 27 33 103 77
CRW_01186 - 0.40 0.34 0.47 131 836292 164 14 134 16 255
CRW_01250 - 0.48 0.39 0.59 147 781625 116 11 92 13 231
CRW_01266 - 0.36 0.34 0.38 129 818217 229 37 177 15 252
CRW_01271 - 0.37 0.32 0.42 122 827252 174 25 142 7 259
CRW_01344 - 0.27 0.22 0.33 81 791667 168 23 140 5 285
PDB_00409 - 0.36 0.40 0.32 98 688245 284 64 144 76 147
PDB_00805 - 0.68 0.60 0.76 182 467790 85 2 54 29 120
PDB_01261 - 0.77 0.64 0.92 216 467794 23 1 17 5 120

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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 3908
Total TN 39592372
Total FP 21488
Total FP CONTRA 3257
Total FP INCONS 13569
Total FP COMP 4662
Total FN 14855
Total Scores
MCC 0.198
Average MCC ± 95% Confidence Intervals 0.215 ± 0.029
Sensitivity 0.208
Positive Predictive Value 0.188
Nr of predictions 77

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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_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_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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