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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric ContextFold RNAwolf
MCC 0.682 > 0.199
Average MCC ± 95% Confidence Intervals 0.667 ± 0.043 > 0.215 ± 0.027
Sensitivity 0.634 > 0.212
Positive Predictive Value 0.733 > 0.188
Total TP 13077 > 4369
Total TN 45327230 > 45321852
Total FP 8589 < 24745
Total FP CONTRA 1113 < 3879
Total FP INCONS 3654 < 14974
Total FP COMP 3822 < 5892
Total FN 7536 < 16244
P-value 3.56938820447e-08

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Performance plots


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

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

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Performance of ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

Total Base Pair Counts
Total TP 13077
Total TN 45327230
Total FP 8589
Total FP CONTRA 1113
Total FP INCONS 3654
Total FP COMP 3822
Total FN 7536
Total Scores
MCC 0.682
Average MCC ± 95% Confidence Intervals 0.667 ± 0.043
Sensitivity 0.634
Positive Predictive Value 0.733
Nr of predictions 88

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00002 - 0.59 0.52 0.69 136 408862 102 9 53 40 128
CRW_00417 - 0.87 0.80 0.95 209 458183 19 2 9 8 53
CRW_00418 - 0.66 0.58 0.75 152 441127 54 6 45 3 108
CRW_00419 - 0.78 0.70 0.88 186 463954 32 6 20 6 79
CRW_00421 - 0.77 0.71 0.84 188 462978 47 6 31 10 78
CRW_00422 - 0.90 0.81 0.99 214 455318 14 0 3 11 49
CRW_00424 - 0.69 0.63 0.77 228 789098 94 11 59 24 135
CRW_00426 - 0.88 0.81 0.97 214 457225 18 0 7 11 51
CRW_00427 - 0.80 0.74 0.88 192 454363 31 5 21 5 69
CRW_00428 - 0.80 0.71 0.89 185 465888 28 2 20 6 75
CRW_00430 - 0.76 0.71 0.83 188 456263 46 7 32 7 78
CRW_00433 - 0.83 0.73 0.94 192 467823 17 2 11 4 71
CRW_00434 - 0.87 0.77 0.97 203 457237 12 3 3 6 60
CRW_00435 - 0.60 0.51 0.69 136 451528 71 6 55 10 129
CRW_00437 - 0.85 0.77 0.94 199 456279 19 1 11 7 61
CRW_00438 - 0.75 0.66 0.84 178 454369 43 5 29 9 90
CRW_00441 - 0.84 0.76 0.93 198 454368 21 1 14 6 64
CRW_00442 - 0.76 0.68 0.84 178 453416 46 4 30 12 83
CRW_00443 - 0.61 0.53 0.70 138 456292 71 7 53 11 122
CRW_00444 - 0.89 0.81 0.98 214 459143 13 2 2 9 49
CRW_00445 - 0.86 0.76 0.97 202 458195 11 1 5 5 63
CRW_00446 - 0.86 0.79 0.93 209 468771 29 3 13 13 56
CRW_00447 - 0.61 0.58 0.66 150 452447 84 15 64 5 110
CRW_00448 - 0.86 0.76 0.97 198 457241 20 1 6 13 63
CRW_00449 - 0.83 0.76 0.91 197 444879 26 7 13 6 63
CRW_00450 - 0.76 0.68 0.84 178 458191 47 6 28 13 84
CRW_00451 - 0.84 0.76 0.92 201 457228 26 4 13 9 63
CRW_00452 - 0.88 0.79 0.98 208 453415 14 3 2 9 54
CRW_00453 - 0.75 0.66 0.86 172 452477 34 3 24 7 89
CRW_00456 - 0.82 0.74 0.91 195 470720 26 2 18 6 70
CRW_00457 - 0.86 0.78 0.95 207 467811 23 3 7 13 57
CRW_00458 - 0.91 0.84 0.98 223 464902 16 2 3 11 41
CRW_00459 - 0.87 0.79 0.96 207 462025 19 0 9 10 56
CRW_00462 - 0.79 0.70 0.88 183 458196 30 6 18 6 78
CRW_00463 - 0.75 0.69 0.82 176 445825 42 11 28 3 78
CRW_00464 - 0.88 0.80 0.97 212 462022 14 2 5 7 52
CRW_00530 - 0.29 0.28 0.30 74 534851 176 43 127 6 194
CRW_00532 - 0.15 0.14 0.15 38 579171 226 55 162 9 227
CRW_00533 - 0.54 0.53 0.56 115 453422 146 34 57 55 104
CRW_00538 - 0.31 0.29 0.34 88 811913 189 31 143 15 212
CRW_00604 - 0.76 0.77 0.76 62 411696 170 7 13 150 19
CRW_00606 - 0.55 0.57 0.54 52 559057 214 15 29 170 40
CRW_00607 - 0.82 0.77 0.88 59 536063 209 0 8 201 18
CRW_00615 - 0.73 0.71 0.75 58 553801 230 14 5 211 24
CRW_00617 - 0.35 0.38 0.32 24 426351 179 22 29 128 40
CRW_00678 - 0.48 0.51 0.45 62 666296 245 14 63 168 59
CRW_00680 - 0.88 0.84 0.92 102 516525 157 3 6 148 20
CRW_00683 - 0.61 0.64 0.58 86 460172 167 26 36 105 49
CRW_00684 - 0.60 0.64 0.56 86 612017 209 26 42 141 49
CRW_00702 - 0.74 0.79 0.69 59 357350 156 19 7 130 16
CRW_00704 - 0.58 0.54 0.61 51 386677 165 11 21 133 43
CRW_00706 - 0.54 0.63 0.47 37 695531 262 23 19 220 22
CRW_00713 - 0.64 0.59 0.70 60 731359 250 4 22 224 41
CRW_00730 - 0.56 0.57 0.55 92 338909 135 20 55 60 69
CRW_00734 - 0.28 0.32 0.25 35 537028 200 40 63 97 75
CRW_00735 - 0.29 0.36 0.23 43 677847 241 75 65 101 78
CRW_00740 - 0.18 0.19 0.17 21 489430 212 17 87 108 92
CRW_00746 - 0.50 0.51 0.49 111 550500 161 34 80 47 108
CRW_00750 - 0.57 0.56 0.57 90 709679 189 15 52 122 70
CRW_00751 - 0.48 0.49 0.47 87 489370 165 33 65 67 91
CRW_00753 - 0.09 0.10 0.09 17 489362 239 44 132 63 161
CRW_00757 - 0.08 0.09 0.07 11 415255 219 48 102 69 115
CRW_00765 - 0.86 0.79 0.93 203 452457 30 4 12 14 54
CRW_00766 - 0.41 0.38 0.45 92 440185 127 14 100 13 148
CRW_00768 - 0.83 0.76 0.92 196 471692 35 1 17 17 63
CRW_00769 - 0.69 0.62 0.78 155 451525 53 9 36 8 97
CRW_00773 - 0.80 0.74 0.87 192 451505 40 1 27 12 67
CRW_00774 - 0.85 0.78 0.94 205 488347 28 1 13 14 58
CRW_00777 - 0.46 0.44 0.48 135 719120 172 28 117 27 169
CRW_00780 - 0.81 0.73 0.90 185 475594 40 5 16 19 70
CRW_00783 - 0.82 0.73 0.93 188 453425 24 2 13 9 71
CRW_00784 - 0.88 0.80 0.96 210 456272 24 2 6 16 52
CRW_00785 - 0.80 0.72 0.88 183 452468 37 3 22 12 70
CRW_00787 - 0.47 0.44 0.50 134 646683 154 23 113 18 172
CRW_00794 - 0.57 0.50 0.64 123 434586 76 10 59 7 123
CRW_00796 - 0.47 0.41 0.55 96 384827 87 6 74 7 139
CRW_00797 - 0.41 0.39 0.44 132 692956 181 21 144 16 210
CRW_00801 - 0.72 0.68 0.76 169 438295 67 11 41 15 80
CRW_00802 - 0.69 0.64 0.75 162 460104 68 15 39 14 91
CRW_00813 - 0.36 0.39 0.33 52 530805 210 44 64 102 81
CRW_01186 - 0.81 0.76 0.87 293 836234 52 8 36 8 93
CRW_01250 - 0.79 0.71 0.88 269 781568 41 5 33 3 109
CRW_01266 - 0.78 0.73 0.84 278 818229 67 5 48 14 103
CRW_01271 - 0.58 0.54 0.63 205 827215 135 18 103 14 176
CRW_01344 - 0.67 0.62 0.73 226 791602 94 9 74 11 140
PDB_00409 - 0.60 0.61 0.60 149 688301 225 27 74 124 96
PDB_00805 - 0.65 0.61 0.69 183 467763 101 10 72 19 119
PDB_01261 - 0.68 0.58 0.79 196 467781 51 4 47 0 140

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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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