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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric Afold RNAwolf
MCC 0.324 > 0.195
Average MCC ± 95% Confidence Intervals 0.344 ± 0.034 > 0.211 ± 0.031
Sensitivity 0.320 > 0.206
Positive Predictive Value 0.329 > 0.185
Total TP 5415 > 3497
Total TN 36224103 > 36221706
Total FP 14521 < 19765
Total FP CONTRA 2001 < 3099
Total FP INCONS 9067 < 12284
Total FP COMP 3453 < 4382
Total FN 11528 < 13446
P-value 3.56938820447e-08

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Performance plots


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

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

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Performance of Afold - scored higher in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP 5415
Total TN 36224103
Total FP 14521
Total FP CONTRA 2001
Total FP INCONS 9067
Total FP COMP 3453
Total FN 11528
Total Scores
MCC 0.324
Average MCC ± 95% Confidence Intervals 0.344 ± 0.034
Sensitivity 0.320
Positive Predictive Value 0.329
Nr of predictions 71

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00002 - 0.55 0.55 0.55 145 408798 132 32 85 15 119
CRW_00417 - 0.38 0.37 0.39 97 458157 161 21 128 12 165
CRW_00418 - 0.24 0.22 0.26 56 441113 170 17 144 9 204
CRW_00419 - 0.19 0.17 0.20 45 463945 187 22 154 11 220
CRW_00421 - 0.38 0.36 0.41 96 462968 155 22 117 16 170
CRW_00422 - 0.36 0.35 0.38 92 455291 171 23 129 19 171
CRW_00426 - 0.30 0.29 0.31 78 457195 183 24 149 10 187
CRW_00427 - 0.18 0.18 0.19 46 454337 212 30 168 14 215
CRW_00428 - 0.39 0.38 0.40 98 465847 162 29 121 12 162
CRW_00430 - 0.18 0.18 0.19 47 456245 207 30 168 9 219
CRW_00433 - 0.35 0.32 0.38 85 467807 142 19 117 6 178
CRW_00434 - 0.38 0.35 0.40 92 457218 146 18 118 10 171
CRW_00435 - 0.36 0.33 0.39 88 451501 148 14 122 12 177
CRW_00437 - 0.21 0.21 0.22 54 456242 197 25 169 3 206
CRW_00438 - 0.35 0.34 0.36 90 454332 170 19 140 11 178
CRW_00441 - 0.17 0.16 0.19 42 454357 187 31 151 5 220
CRW_00442 - 0.37 0.36 0.39 93 453388 156 25 122 9 168
CRW_00443 - 0.39 0.36 0.42 93 456266 153 18 113 22 167
CRW_00444 - 0.27 0.26 0.28 68 459119 181 24 150 7 195
CRW_00445 - 0.28 0.27 0.30 71 458168 175 24 140 11 194
CRW_00446 - 0.46 0.43 0.48 115 468758 135 14 109 12 150
CRW_00447 - 0.27 0.27 0.28 69 452428 194 23 156 15 191
CRW_00448 - 0.34 0.32 0.36 83 457215 169 23 125 21 178
CRW_00449 - 0.22 0.21 0.23 54 444861 185 20 161 4 206
CRW_00451 - 0.21 0.20 0.21 52 457204 204 25 165 14 212
CRW_00452 - 0.31 0.29 0.34 77 453399 174 20 132 22 185
CRW_00453 - 0.34 0.31 0.36 81 452454 150 22 119 9 180
CRW_00458 - 0.32 0.31 0.32 83 464873 185 34 140 11 181
CRW_00459 - 0.29 0.27 0.31 72 462011 176 27 131 18 191
CRW_00462 - 0.28 0.27 0.30 70 458171 178 16 146 16 191
CRW_00463 - 0.34 0.33 0.35 85 445799 164 22 134 8 169
CRW_00464 - 0.39 0.36 0.42 95 462015 142 15 116 11 169
CRW_00530 - 0.35 0.37 0.33 99 534792 223 55 149 19 169
CRW_00532 - 0.12 0.14 0.11 36 579108 293 84 198 11 229
CRW_00538 - 0.20 0.22 0.19 65 811827 304 77 206 21 235
CRW_00604 - 0.52 0.57 0.48 46 411682 214 15 35 164 35
CRW_00606 - 0.66 0.64 0.68 59 559066 266 2 26 238 33
CRW_00607 - 0.55 0.53 0.56 41 536057 274 4 28 242 36
CRW_00617 - 0.66 0.64 0.68 41 426366 236 1 18 217 23
CRW_00678 - 0.66 0.64 0.67 78 666318 274 10 29 235 43
CRW_00684 - 0.34 0.39 0.29 53 611990 298 44 84 170 82
CRW_00704 - 0.81 0.80 0.82 75 386669 198 4 12 182 19
CRW_00706 - 0.45 0.51 0.39 30 695534 340 11 35 294 29
CRW_00713 - 0.56 0.57 0.55 58 731339 313 11 37 265 43
CRW_00730 - 0.46 0.52 0.41 84 338869 186 39 84 63 77
CRW_00734 - 0.18 0.25 0.13 27 536961 263 99 79 85 83
CRW_00735 - 0.26 0.33 0.20 40 677832 298 85 73 140 81
CRW_00740 - 0.00 0.00 0.00 0 489332 297 100 123 74 113
CRW_00746 - 0.45 0.47 0.44 102 550492 206 29 102 75 117
CRW_00750 - 0.39 0.44 0.35 71 709632 301 38 95 168 89
CRW_00753 - 0.15 0.16 0.14 29 489341 277 47 138 92 149
CRW_00766 - 0.27 0.26 0.28 63 440168 177 20 140 17 177
CRW_00768 - 0.40 0.39 0.41 101 471658 164 22 125 17 158
CRW_00769 - 0.39 0.37 0.42 93 451502 148 20 110 18 159
CRW_00774 - 0.37 0.36 0.39 94 488322 170 17 133 20 169
CRW_00780 - 0.18 0.18 0.19 45 475569 201 21 165 15 210
CRW_00783 - 0.37 0.36 0.38 93 453382 165 15 138 12 166
CRW_00784 - 0.37 0.35 0.39 93 456254 166 21 122 23 169
CRW_00785 - 0.35 0.33 0.36 84 452443 162 27 122 13 169
CRW_00787 - 0.23 0.24 0.23 74 646626 267 36 217 14 232
CRW_00794 - 0.24 0.24 0.25 59 434543 196 15 161 20 187
CRW_00796 - 0.20 0.20 0.21 47 384777 193 27 152 14 188
CRW_00797 - 0.26 0.26 0.26 90 692907 280 33 223 24 252
CRW_00801 - 0.45 0.45 0.46 112 438270 149 29 105 15 137
CRW_00802 - 0.19 0.19 0.19 49 460062 218 33 176 9 204
CRW_01186 - 0.27 0.27 0.27 103 836190 293 44 234 15 283
CRW_01250 - 0.31 0.30 0.32 115 781518 257 33 209 15 263
CRW_01266 - 0.28 0.28 0.28 108 818174 292 43 235 14 273
CRW_01344 - 0.30 0.30 0.30 110 791545 267 40 216 11 256
PDB_00805 - 0.64 0.61 0.67 184 467752 116 18 74 24 118
PDB_01261 - 0.50 0.45 0.55 152 467752 128 4 120 4 184

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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 3497
Total TN 36221706
Total FP 19765
Total FP CONTRA 3099
Total FP INCONS 12284
Total FP COMP 4382
Total FN 13446
Total Scores
MCC 0.195
Average MCC ± 95% Confidence Intervals 0.211 ± 0.031
Sensitivity 0.206
Positive Predictive Value 0.185
Nr of predictions 71

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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_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_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_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_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_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_00684 - 0.10 0.13 0.09 17 611976 357 48 130 179 118
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_00753 - 0.09 0.10 0.08 18 489326 306 44 167 95 160
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_00774 - 0.15 0.16 0.14 42 488276 276 32 216 28 221
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_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_01344 - 0.16 0.16 0.16 59 791531 333 54 267 12 307
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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