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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric RNAfold RNAwolf
MCC 0.329 > 0.198
Average MCC ± 95% Confidence Intervals 0.352 ± 0.032 > 0.215 ± 0.029
Sensitivity 0.323 > 0.208
Positive Predictive Value 0.336 > 0.188
Total TP 6068 > 3908
Total TN 39595042 > 39592372
Total FP 15762 < 21488
Total FP CONTRA 1944 < 3257
Total FP INCONS 10052 < 13569
Total FP COMP 3766 < 4662
Total FN 12695 < 14855
P-value 3.56938820447e-08

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Performance plots


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

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

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Performance of RNAfold - scored higher in this pairwise comparison

1. Total counts & total scores for RNAfold

Total Base Pair Counts
Total TP 6068
Total TN 39595042
Total FP 15762
Total FP CONTRA 1944
Total FP INCONS 10052
Total FP COMP 3766
Total FN 12695
Total Scores
MCC 0.329
Average MCC ± 95% Confidence Intervals 0.352 ± 0.032
Sensitivity 0.323
Positive Predictive Value 0.336
Nr of predictions 77

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00002 - 0.50 0.49 0.50 130 408802 144 31 97 16 134
CRW_00417 - 0.38 0.37 0.39 97 458157 160 21 128 11 165
CRW_00418 - 0.21 0.20 0.23 51 441107 179 25 147 7 209
CRW_00419 - 0.22 0.21 0.23 55 463931 187 18 162 7 210
CRW_00421 - 0.34 0.32 0.36 86 462964 166 22 131 13 180
CRW_00422 - 0.26 0.25 0.28 65 455302 185 23 145 17 198
CRW_00424 - 0.38 0.38 0.37 138 789026 258 22 210 26 225
CRW_00426 - 0.40 0.38 0.41 102 457198 158 27 119 12 163
CRW_00427 - 0.21 0.21 0.22 54 454333 207 33 161 13 207
CRW_00428 - 0.39 0.38 0.40 98 465850 158 28 119 11 162
CRW_00430 - 0.22 0.21 0.23 56 456245 198 23 166 9 210
CRW_00433 - 0.29 0.26 0.33 69 467817 147 21 121 5 194
CRW_00434 - 0.39 0.36 0.42 94 457220 142 17 115 10 169
CRW_00435 - 0.32 0.30 0.33 80 451486 161 19 140 2 185
CRW_00437 - 0.21 0.21 0.22 54 456242 201 25 169 7 206
CRW_00438 - 0.35 0.34 0.37 90 454335 166 19 137 10 178
CRW_00441 - 0.25 0.23 0.27 61 454355 169 27 138 4 201
CRW_00442 - 0.37 0.36 0.39 94 453386 156 25 123 8 167
CRW_00443 - 0.39 0.36 0.42 93 456267 151 22 108 21 167
CRW_00444 - 0.25 0.24 0.27 63 459128 178 32 138 8 200
CRW_00445 - 0.26 0.25 0.28 65 458167 180 24 147 9 200
CRW_00446 - 0.52 0.49 0.56 131 468760 121 11 94 16 134
CRW_00447 - 0.30 0.28 0.31 74 452437 184 17 148 19 186
CRW_00448 - 0.35 0.34 0.37 88 457211 166 26 121 19 173
CRW_00449 - 0.28 0.27 0.29 71 444849 178 27 149 2 189
CRW_00450 - 0.32 0.30 0.34 78 458171 169 22 132 15 184
CRW_00451 - 0.21 0.20 0.21 52 457204 203 26 164 13 212
CRW_00452 - 0.26 0.25 0.28 66 453389 185 27 146 12 196
CRW_00453 - 0.27 0.25 0.29 65 452448 171 30 133 8 196
CRW_00456 - 0.45 0.42 0.48 112 470704 135 20 99 16 153
CRW_00457 - 0.34 0.32 0.37 85 467798 158 17 128 13 179
CRW_00458 - 0.37 0.35 0.38 93 464886 163 30 121 12 171
CRW_00459 - 0.29 0.27 0.31 72 462008 178 27 134 17 191
CRW_00462 - 0.14 0.13 0.14 34 458165 214 27 177 10 227
CRW_00463 - 0.28 0.28 0.29 71 445794 181 25 150 6 183
CRW_00464 - 0.39 0.36 0.42 95 462015 141 15 116 10 169
CRW_00530 - 0.29 0.31 0.27 82 534794 236 54 165 17 186
CRW_00538 - 0.19 0.21 0.18 63 811827 305 77 208 20 237
CRW_00604 - 0.52 0.57 0.48 46 411682 217 15 35 167 35
CRW_00606 - 0.66 0.64 0.69 59 559067 263 2 25 236 33
CRW_00607 - 0.54 0.55 0.53 42 536050 277 8 30 239 35
CRW_00615 - 0.50 0.56 0.44 46 553773 284 24 35 225 36
CRW_00617 - 0.27 0.31 0.24 20 426343 263 19 44 200 44
CRW_00678 - 0.64 0.64 0.64 77 666315 276 10 33 233 44
CRW_00680 - 0.66 0.68 0.64 83 516507 213 8 38 167 39
CRW_00683 - 0.40 0.41 0.38 55 460177 239 20 68 151 80
CRW_00684 - 0.36 0.39 0.33 53 612010 292 37 71 184 82
CRW_00702 - 0.66 0.72 0.61 54 357347 206 10 24 172 21
CRW_00704 - 0.81 0.80 0.82 75 386669 196 4 12 180 19
CRW_00706 - 0.37 0.41 0.34 24 695540 344 7 39 298 35
CRW_00713 - 0.67 0.65 0.69 66 731349 302 5 25 272 35
CRW_00765 - 0.44 0.44 0.45 113 452424 156 21 118 17 144
CRW_00766 - 0.22 0.22 0.23 52 440167 190 20 152 18 188
CRW_00768 - 0.50 0.48 0.51 125 471661 142 15 105 22 134
CRW_00769 - 0.39 0.37 0.42 93 451501 148 21 110 17 159
CRW_00773 - 0.34 0.34 0.33 88 451460 186 30 147 9 171
CRW_00774 - 0.27 0.27 0.28 70 488320 198 15 161 22 193
CRW_00777 - 0.24 0.25 0.23 77 719060 291 60 203 28 227
CRW_00780 - 0.20 0.19 0.21 49 475564 199 20 167 12 206
CRW_00783 - 0.31 0.31 0.32 80 453377 182 16 155 11 179
CRW_00784 - 0.36 0.34 0.38 90 456253 169 22 125 22 172
CRW_00785 - 0.35 0.33 0.36 84 452443 161 27 122 12 169
CRW_00787 - 0.23 0.24 0.22 72 646627 264 41 213 10 234
CRW_00794 - 0.24 0.24 0.24 58 434537 202 18 165 19 188
CRW_00796 - 0.20 0.20 0.21 47 384780 189 27 149 13 188
CRW_00797 - 0.22 0.23 0.21 79 692885 304 40 249 15 263
CRW_00801 - 0.43 0.43 0.43 106 438270 153 32 108 13 143
CRW_00802 - 0.30 0.30 0.31 75 460080 183 33 132 18 178
CRW_00813 - 0.13 0.15 0.11 20 530775 316 43 127 146 113
CRW_01186 - 0.29 0.30 0.29 114 836184 292 36 237 19 272
CRW_01250 - 0.24 0.24 0.24 90 781502 295 38 245 12 288
CRW_01266 - 0.25 0.26 0.25 99 818161 313 44 256 13 282
CRW_01271 - 0.33 0.34 0.33 129 827149 276 38 225 13 252
CRW_01344 - 0.32 0.32 0.32 116 791548 261 44 203 14 250
PDB_00409 - 0.25 0.29 0.21 71 688215 334 71 194 69 174
PDB_00805 - 0.65 0.64 0.67 192 467742 117 17 77 23 110
PDB_01261 - 0.50 0.45 0.55 152 467750 130 4 122 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 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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