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Table of contents:

  1. Overview

  2. Performance Plots

  3. Performance of RNAalifold(20) - scored higher in this pairwise comparison

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

  5. Compile and download dataset for RNAalifold(20) & Fold [.zip] - may take several seconds...


Overview

Metric RNAalifold(20) Fold
MCC 0.674 > 0.385
Average MCC ± 95% Confidence Intervals 0.674 ± 0.044 > 0.388 ± 0.024
Sensitivity 0.621 > 0.390
Positive Predictive Value 0.732 > 0.381
Total TP 22941 > 14429
Total TN 104339145 > 104332585
Total FP 9959 < 26119
Total FP CONTRA 1517 < 3646
Total FP INCONS 6863 < 19806
Total FP COMP 1579 < 2667
Total FN 14023 < 22535
P-value 3.56938820447e-08

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Performance plots


  1. Comparison of performance of RNAalifold(20) and Fold. 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 RNAalifold(20) and Fold).

  2. Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for RNAalifold(20) and Fold).

  3. Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(20) and Fold. 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 RNAalifold(20) and Fold).

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Performance of RNAalifold(20) - scored higher in this pairwise comparison

1. Total counts & total scores for RNAalifold(20)

Total Base Pair Counts
Total TP 22941
Total TN 104339145
Total FP 9959
Total FP CONTRA 1517
Total FP INCONS 6863
Total FP COMP 1579
Total FN 14023
Total Scores
MCC 0.674
Average MCC ± 95% Confidence Intervals 0.674 ± 0.044
Sensitivity 0.621
Positive Predictive Value 0.732
Nr of predictions 77

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2. Individual counts for RNAalifold(20) [ download as .csv ]

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.87 0.84 0.90 385 1085172 61 7 37 17 73
CRW_00034 0.83 0.78 0.87 371 1141890 74 12 43 19 103
CRW_00048 0.83 0.80 0.86 374 1170779 75 11 51 13 96
CRW_00054 0.84 0.82 0.87 372 1107390 68 12 42 14 84
CRW_00059 0.81 0.76 0.86 361 1172324 71 11 50 10 112
CRW_00061 0.85 0.80 0.90 382 1181529 55 14 28 13 94
CRW_00068 0.86 0.83 0.89 381 1108875 61 12 37 12 76
CRW_00096 0.85 0.81 0.90 376 1178461 63 6 37 20 89
CRW_00140 0.84 0.82 0.87 380 1135841 71 13 44 14 83
CRW_00141 0.82 0.78 0.87 371 1201597 71 12 45 14 105
CRW_00150 0.84 0.80 0.88 372 1152500 62 12 37 13 94
CRW_00152 0.79 0.75 0.82 355 1179984 91 17 60 14 116
CRW_00166 0.83 0.79 0.88 368 1190777 71 7 44 20 100
CRW_00173 0.77 0.75 0.80 332 1082242 94 12 70 12 113
CRW_00177 0.80 0.76 0.84 358 1178455 78 13 54 11 115
CRW_00196 0.82 0.79 0.86 373 1207803 68 15 44 9 102
CRW_00230 0.83 0.79 0.88 378 1198495 67 12 41 14 100
CRW_00245 0.86 0.83 0.89 378 1105903 56 14 33 9 75
CRW_00248 0.79 0.75 0.83 364 1218705 87 17 55 15 120
CRW_00250 0.83 0.78 0.88 373 1198502 61 12 39 10 105
CRW_00256 0.82 0.78 0.87 363 1192322 68 14 41 13 105
CRW_00270 0.85 0.83 0.88 376 1111859 66 12 39 15 79
CRW_00271 0.82 0.79 0.87 363 1122332 69 11 45 13 99
CRW_00273 0.84 0.81 0.87 360 1085185 68 13 43 12 86
CRW_00275 0.84 0.81 0.87 368 1114849 68 12 42 14 89
CRW_00277 0.82 0.79 0.85 359 1110374 76 14 48 14 94
CRW_00278 0.82 0.78 0.86 349 1129851 72 10 46 16 101
CRW_00279 0.81 0.78 0.85 360 1179994 80 12 50 18 104
CRW_00280 0.83 0.79 0.87 360 1117845 71 12 43 16 93
CRW_00281 0.82 0.78 0.85 363 1144916 75 12 50 13 101
CRW_00284 0.84 0.80 0.89 363 1131350 62 12 35 15 93
CRW_00285 0.83 0.79 0.88 364 1117844 66 13 39 14 94
CRW_00289 0.81 0.76 0.86 361 1189232 70 13 47 10 115
CRW_00298 0.43 0.38 0.49 187 1620517 224 43 153 28 307
CRW_00301 0.42 0.37 0.48 192 1762101 229 37 173 19 327
CRW_00306 0.42 0.38 0.46 176 1445467 237 39 168 30 286
CRW_00310 0.46 0.39 0.55 204 1805579 190 29 138 23 317
CRW_00326 0.41 0.35 0.47 178 1627730 219 36 166 17 324
CRW_00330 0.40 0.35 0.47 182 1988624 243 35 174 34 335
CRW_00332 0.39 0.34 0.43 164 1769642 239 35 180 24 313
CRW_00333 0.34 0.29 0.40 150 1892114 241 34 187 20 364
CRW_00345 0.43 0.38 0.48 189 1586477 222 39 166 17 309
CRW_00346 0.45 0.40 0.50 202 1584688 230 32 168 30 299
CRW_00348 0.43 0.38 0.48 190 1615106 228 41 166 21 313
CRW_00358 0.43 0.38 0.49 192 1674972 227 34 167 26 315
CRW_00366 0.39 0.34 0.45 166 1579381 248 30 176 42 316
CRW_00370 0.52 0.47 0.57 240 1640342 204 34 150 20 266
CRW_00371 0.43 0.38 0.49 187 1611527 222 27 169 26 309
CRW_00372 0.40 0.35 0.46 174 1625925 228 37 170 21 324
CRW_00379 0.40 0.34 0.47 179 2126574 228 31 169 28 355
CRW_00386 0.44 0.37 0.51 193 1750879 199 35 149 15 322
CRW_00403 0.39 0.37 0.42 170 1606127 272 38 193 41 294
CRW_00411 0.43 0.39 0.48 191 1615105 227 43 164 20 305
CRW_00414 0.38 0.35 0.41 171 1665811 266 36 207 23 324
CRW_00466 0.84 0.81 0.86 373 1116333 74 11 48 15 85
CRW_00589 0.86 0.81 0.91 361 1094062 61 7 30 24 84
CRW_00590 0.84 0.79 0.89 358 1119354 70 6 38 26 94
CRW_00591 0.87 0.83 0.91 368 1098500 61 9 26 26 78
CRW_00598 0.42 0.38 0.47 187 1665825 229 39 174 16 304
CRW_00758 0.48 0.43 0.53 210 1640373 205 34 149 22 273
CRW_00759 0.42 0.38 0.48 182 1636762 232 39 162 31 299
CRW_00760 0.43 0.37 0.50 179 1638594 209 38 144 27 307
CRW_00772 0.78 0.74 0.83 298 945642 94 6 54 34 106
CRW_00789 0.82 0.78 0.87 348 1137388 80 6 44 30 99
CRW_00795 0.74 0.70 0.79 276 1152572 131 10 63 58 118
CRW_00849 0.78 0.74 0.82 350 1117832 97 13 65 19 120
CRW_00997 0.84 0.81 0.88 374 1135854 61 12 38 11 90
CRW_01153 0.47 0.42 0.53 210 1606133 216 27 158 31 293
CRW_01171 0.44 0.38 0.50 193 1593619 210 32 161 17 313
CRW_01300 0.52 0.45 0.59 231 1693331 174 31 127 16 284
PDB_00703 0.78 0.71 0.86 353 1073436 80 10 46 24 142
PDB_00854 0.75 0.65 0.86 347 1500373 97 7 51 39 188
PDB_01088 0.73 0.62 0.86 341 1471072 93 2 55 36 206
PDB_01103 0.75 0.65 0.87 364 1606111 77 8 45 24 198
PDB_01105 0.76 0.67 0.87 360 1433555 85 3 53 29 180
PDB_01120 0.72 0.65 0.80 341 1204702 101 13 72 16 186
PDB_01273 0.78 0.71 0.86 347 1117857 83 8 48 27 144

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Performance of Fold - scored lower in this pairwise comparison

1. Total counts & total scores for Fold

Total Base Pair Counts
Total TP 14429
Total TN 104332585
Total FP 26119
Total FP CONTRA 3646
Total FP INCONS 19806
Total FP COMP 2667
Total FN 22535
Total Scores
MCC 0.385
Average MCC ± 95% Confidence Intervals 0.388 ± 0.024
Sensitivity 0.390
Positive Predictive Value 0.381
Nr of predictions 77

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.56 0.57 0.56 259 1085140 238 22 180 36 199
CRW_00034 0.62 0.63 0.61 299 1141829 219 35 153 31 175
CRW_00048 0.51 0.51 0.52 239 1170753 241 24 199 18 231
CRW_00054 0.40 0.41 0.40 185 1107355 286 30 246 10 271
CRW_00059 0.44 0.44 0.44 207 1172278 279 31 230 18 266
CRW_00061 0.54 0.54 0.54 259 1181475 236 33 186 17 217
CRW_00068 0.43 0.43 0.43 198 1108845 279 32 230 17 259
CRW_00096 0.42 0.43 0.42 200 1178403 299 28 249 22 265
CRW_00140 0.38 0.38 0.38 176 1135818 299 27 257 15 287
CRW_00141 0.53 0.53 0.54 253 1201553 246 34 185 27 223
CRW_00150 0.45 0.44 0.45 204 1152472 262 26 219 17 262
CRW_00152 0.53 0.52 0.54 246 1179962 231 33 175 23 225
CRW_00166 0.40 0.40 0.39 188 1190720 309 32 256 21 280
CRW_00173 0.28 0.28 0.28 125 1082214 333 31 286 16 320
CRW_00177 0.49 0.48 0.50 226 1178426 251 26 202 23 247
CRW_00196 0.45 0.46 0.44 219 1207740 296 42 234 20 256
CRW_00230 0.53 0.52 0.54 247 1198465 241 32 182 27 231
CRW_00245 0.37 0.37 0.37 167 1105882 297 32 247 18 286
CRW_00248 0.49 0.49 0.48 238 1218645 286 36 222 28 246
CRW_00250 0.37 0.38 0.37 181 1198432 321 48 265 8 297
CRW_00256 0.39 0.39 0.40 183 1192281 294 41 235 18 285
CRW_00270 0.54 0.54 0.54 245 1111832 232 27 182 23 210
CRW_00271 0.36 0.36 0.37 168 1122293 309 37 253 19 294
CRW_00273 0.52 0.52 0.52 233 1085151 238 41 176 21 213
CRW_00275 0.59 0.59 0.59 271 1114809 212 28 163 21 186
CRW_00277 0.32 0.32 0.32 144 1110348 313 38 265 10 309
CRW_00278 0.36 0.35 0.37 159 1129828 293 31 238 24 291
CRW_00279 0.58 0.56 0.59 262 1179969 207 27 158 22 202
CRW_00280 0.33 0.33 0.32 151 1117794 327 43 272 12 302
CRW_00281 0.53 0.52 0.53 243 1144885 238 27 186 25 221
CRW_00284 0.29 0.29 0.29 130 1131315 331 40 275 16 326
CRW_00285 0.48 0.49 0.48 225 1117789 265 38 208 19 233
CRW_00289 0.51 0.50 0.52 237 1189193 251 38 185 28 239
CRW_00298 0.22 0.24 0.21 118 1620334 479 100 348 31 376
CRW_00301 0.29 0.30 0.29 156 1761959 461 80 308 73 363
CRW_00306 0.09 0.09 0.08 43 1445337 532 80 390 62 419
CRW_00310 0.28 0.29 0.27 153 1805378 473 77 342 54 368
CRW_00326 0.40 0.40 0.39 203 1627589 370 67 251 52 299
CRW_00330 0.31 0.32 0.30 166 1988453 469 82 314 73 351
CRW_00332 0.19 0.21 0.18 99 1769473 516 102 347 67 378
CRW_00333 0.32 0.33 0.31 169 1891947 449 66 303 80 345
CRW_00345 0.33 0.34 0.33 171 1586345 407 61 294 52 327
CRW_00346 0.33 0.35 0.32 175 1584535 423 75 305 43 326
CRW_00348 0.28 0.28 0.27 142 1614977 433 60 324 49 361
CRW_00358 0.36 0.37 0.35 186 1674831 392 68 280 44 321
CRW_00366 0.27 0.29 0.25 138 1579211 437 87 317 33 344
CRW_00370 0.28 0.29 0.27 148 1640226 440 80 312 48 358
CRW_00371 0.34 0.35 0.33 173 1611383 414 61 293 60 323
CRW_00372 0.26 0.28 0.25 137 1625762 453 84 323 46 361
CRW_00379 0.44 0.45 0.44 241 2126401 411 60 251 100 293
CRW_00386 0.29 0.30 0.28 155 1750699 443 74 328 41 360
CRW_00403 0.33 0.34 0.33 157 1606045 425 57 269 99 307
CRW_00411 0.35 0.36 0.34 177 1614982 392 60 284 48 319
CRW_00414 0.29 0.31 0.28 152 1665688 448 68 317 63 343
CRW_00466 0.57 0.56 0.57 257 1116315 221 28 165 28 201
CRW_00589 0.30 0.30 0.31 133 1094029 317 35 263 19 312
CRW_00590 0.42 0.42 0.42 191 1119306 279 34 225 20 261
CRW_00591 0.50 0.50 0.50 222 1098458 256 20 203 33 224
CRW_00598 0.35 0.37 0.34 181 1665691 415 68 285 62 310
CRW_00758 0.25 0.26 0.24 127 1640244 444 62 333 49 356
CRW_00759 0.31 0.32 0.29 156 1636612 443 67 310 66 325
CRW_00760 0.27 0.29 0.26 140 1638417 454 75 323 56 346
CRW_00772 0.25 0.25 0.25 100 945594 319 37 269 13 304
CRW_00789 0.39 0.38 0.39 172 1137342 303 31 241 31 275
CRW_00795 0.32 0.33 0.30 130 1152494 342 43 254 45 264
CRW_00849 0.53 0.53 0.52 250 1117779 255 29 202 24 220
CRW_00997 0.37 0.38 0.37 175 1135806 315 41 256 18 289
CRW_01153 0.36 0.37 0.35 187 1605990 391 60 291 40 316
CRW_01171 0.28 0.28 0.27 143 1593476 430 75 311 44 363
CRW_01300 0.28 0.29 0.27 150 1693165 443 63 342 38 365
PDB_00703 0.48 0.46 0.50 229 1073385 256 28 203 25 266
PDB_00854 0.46 0.46 0.46 246 1500244 334 36 252 46 289
PDB_01088 0.34 0.33 0.34 180 1470946 368 36 308 24 367
PDB_01103 0.44 0.44 0.44 245 1605966 343 42 275 26 317
PDB_01105 0.46 0.45 0.47 245 1433450 306 32 244 30 295
PDB_01120 0.31 0.30 0.33 158 1204643 339 37 290 12 369
PDB_01273 0.38 0.38 0.39 186 1117784 320 28 262 30 305

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Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.