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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric Contrafold RNAwolf
MCC 0.435 > 0.198
Average MCC ± 95% Confidence Intervals 0.465 ± 0.036 > 0.215 ± 0.029
Sensitivity 0.397 > 0.208
Positive Predictive Value 0.478 > 0.188
Total TP 7448 > 3908
Total TN 39597515 > 39592372
Total FP 12148 < 21488
Total FP CONTRA 1218 < 3257
Total FP INCONS 6925 < 13569
Total FP COMP 4005 < 4662
Total FN 11315 < 14855
P-value 3.56938820447e-08

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Performance plots


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

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

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Performance of Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP 7448
Total TN 39597515
Total FP 12148
Total FP CONTRA 1218
Total FP INCONS 6925
Total FP COMP 4005
Total FN 11315
Total Scores
MCC 0.435
Average MCC ± 95% Confidence Intervals 0.465 ± 0.036
Sensitivity 0.397
Positive Predictive Value 0.478
Nr of predictions 77

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00002 - 0.72 0.62 0.82 164 408861 79 5 30 44 100
CRW_00417 - 0.41 0.38 0.44 99 458178 135 23 103 9 163
CRW_00418 - 0.26 0.22 0.31 56 441150 130 14 110 6 204
CRW_00419 - 0.40 0.35 0.45 93 463958 122 7 108 7 172
CRW_00421 - 0.50 0.44 0.57 117 462998 111 10 78 23 149
CRW_00422 - 0.44 0.40 0.49 105 455320 131 13 97 21 158
CRW_00424 - 0.49 0.45 0.52 164 789083 172 18 131 23 199
CRW_00426 - 0.42 0.39 0.45 103 457219 137 13 111 13 162
CRW_00427 - 0.28 0.26 0.29 69 454346 182 30 136 16 192
CRW_00428 - 0.37 0.33 0.40 87 465879 144 17 112 15 173
CRW_00430 - 0.39 0.32 0.48 85 456313 101 17 75 9 181
CRW_00433 - 0.33 0.28 0.40 73 467844 115 12 99 4 190
CRW_00434 - 0.48 0.40 0.56 106 457257 91 9 74 8 157
CRW_00435 - 0.30 0.26 0.34 68 451527 139 21 109 9 197
CRW_00437 - 0.25 0.22 0.29 57 456294 151 16 123 12 203
CRW_00438 - 0.39 0.34 0.44 92 454372 126 15 102 9 176
CRW_00441 - 0.37 0.31 0.44 80 454400 110 12 89 9 182
CRW_00442 - 0.32 0.28 0.37 74 453426 139 14 114 11 187
CRW_00443 - 0.34 0.26 0.43 68 456333 107 8 81 18 192
CRW_00444 - 0.45 0.38 0.53 100 459174 99 15 72 12 163
CRW_00445 - 0.43 0.40 0.47 105 458179 127 19 100 8 160
CRW_00446 - 0.33 0.31 0.36 81 468771 157 18 126 13 184
CRW_00447 - 0.29 0.27 0.30 71 452442 174 23 140 11 189
CRW_00448 - 0.29 0.26 0.34 67 457247 143 23 109 11 194
CRW_00449 - 0.42 0.37 0.48 95 444897 111 20 84 7 165
CRW_00450 - 0.43 0.36 0.53 94 458224 101 11 74 16 168
CRW_00451 - 0.43 0.38 0.49 99 457244 114 11 92 11 165
CRW_00452 - 0.49 0.41 0.59 108 453445 94 7 68 19 154
CRW_00453 - 0.38 0.32 0.44 84 452487 117 13 92 12 177
CRW_00456 - 0.45 0.37 0.56 98 470760 83 10 67 6 167
CRW_00457 - 0.44 0.41 0.48 107 467803 134 17 101 16 157
CRW_00458 - 0.48 0.42 0.54 111 464926 106 9 84 13 153
CRW_00459 - 0.52 0.46 0.58 121 462032 112 10 78 24 142
CRW_00462 - 0.46 0.40 0.53 104 458208 107 10 81 16 157
CRW_00463 - 0.44 0.40 0.49 101 445832 116 18 89 9 153
CRW_00464 - 0.46 0.38 0.55 101 462056 95 8 76 11 163
CRW_00530 - 0.35 0.34 0.37 91 534848 170 47 109 14 177
CRW_00538 - 0.41 0.38 0.45 113 811923 164 23 116 25 187
CRW_00604 - 0.84 0.85 0.82 69 411694 186 4 11 171 12
CRW_00606 - 0.93 0.90 0.97 83 559067 236 0 3 233 9
CRW_00607 - 0.81 0.82 0.81 63 536052 269 3 12 254 14
CRW_00615 - 0.86 0.85 0.88 70 553798 271 0 10 261 12
CRW_00617 - 0.57 0.55 0.60 35 426368 211 6 17 188 29
CRW_00678 - 0.42 0.44 0.40 53 666302 315 14 66 235 68
CRW_00680 - 0.53 0.55 0.52 67 516506 229 17 46 166 55
CRW_00683 - 0.63 0.63 0.63 85 460186 216 2 47 167 50
CRW_00684 - 0.53 0.55 0.51 74 612025 266 16 56 194 61
CRW_00702 - 0.72 0.73 0.71 55 357357 187 7 16 164 20
CRW_00704 - 0.87 0.87 0.87 82 386666 195 4 8 183 12
CRW_00706 - 0.64 0.71 0.58 42 695537 308 13 18 277 17
CRW_00713 - 0.80 0.77 0.84 78 731352 295 5 10 280 23
CRW_00765 - 0.43 0.39 0.47 101 452459 126 21 95 10 156
CRW_00766 - 0.27 0.23 0.31 56 440213 138 20 102 16 184
CRW_00768 - 0.61 0.55 0.68 143 471695 100 7 61 32 116
CRW_00769 - 0.48 0.43 0.53 108 451522 115 21 74 20 144
CRW_00773 - 0.48 0.45 0.51 116 451497 135 19 93 23 143
CRW_00774 - 0.44 0.40 0.49 105 488352 131 8 101 22 158
CRW_00777 - 0.43 0.42 0.45 127 719119 199 27 127 45 177
CRW_00780 - 0.32 0.29 0.35 74 475591 151 18 117 16 181
CRW_00783 - 0.39 0.33 0.45 86 453437 121 12 93 16 173
CRW_00784 - 0.41 0.37 0.45 96 456279 134 19 96 19 166
CRW_00785 - 0.54 0.48 0.62 122 452478 89 12 64 13 131
CRW_00787 - 0.49 0.45 0.53 138 646691 151 13 111 27 168
CRW_00794 - 0.37 0.35 0.39 85 434558 154 20 115 19 161
CRW_00796 - 0.36 0.29 0.45 69 384851 109 2 81 26 166
CRW_00797 - 0.33 0.30 0.38 101 692984 189 25 143 21 241
CRW_00801 - 0.47 0.45 0.49 113 438286 131 27 90 14 136
CRW_00802 - 0.42 0.39 0.45 99 460102 145 19 100 26 154
CRW_00813 - 0.44 0.47 0.41 63 530812 220 29 61 130 70
CRW_01186 - 0.40 0.38 0.42 146 836224 219 23 178 18 240
CRW_01250 - 0.45 0.41 0.49 155 781556 186 19 145 22 223
CRW_01266 - 0.35 0.35 0.34 134 818168 277 41 217 19 247
CRW_01271 - 0.32 0.32 0.32 121 827157 280 31 232 17 260
CRW_01344 - 0.28 0.27 0.30 98 791579 243 31 203 9 268
PDB_00409 - 0.35 0.40 0.30 99 688225 317 68 159 90 146
PDB_00805 - 0.66 0.64 0.68 193 467745 126 7 83 36 109
PDB_01261 - 0.79 0.69 0.90 233 467769 32 2 24 6 103

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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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