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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 MXScarna(20) - scored lower in this pairwise comparison

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


Overview

Metric RNAalifold(20) MXScarna(20)
MCC 0.674 > 0.598
Average MCC ± 95% Confidence Intervals 0.674 ± 0.044 > 0.603 ± 0.029
Sensitivity 0.621 > 0.548
Positive Predictive Value 0.732 > 0.653
Total TP 22941 > 20251
Total TN 104339145 < 104339447
Total FP 9959 < 14477
Total FP CONTRA 1517 < 1798
Total FP INCONS 6863 < 8970
Total FP COMP 1579 < 3709
Total FN 14023 < 16713
P-value 3.56938820447e-08

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Performance plots


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

  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 MXScarna(20)).

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

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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 MXScarna(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP 20251
Total TN 104339447
Total FP 14477
Total FP CONTRA 1798
Total FP INCONS 8970
Total FP COMP 3709
Total FN 16713
Total Scores
MCC 0.598
Average MCC ± 95% Confidence Intervals 0.603 ± 0.029
Sensitivity 0.548
Positive Predictive Value 0.653
Nr of predictions 77

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.84 0.81 0.87 369 1085176 107 10 46 51 89
CRW_00034 0.68 0.60 0.77 283 1141947 122 12 74 36 191
CRW_00048 0.72 0.67 0.78 317 1170807 127 11 80 36 153
CRW_00054 0.68 0.63 0.74 288 1107425 137 16 87 34 168
CRW_00059 0.72 0.66 0.78 312 1172344 127 16 74 37 161
CRW_00061 0.73 0.66 0.81 316 1181563 109 13 61 35 160
CRW_00068 0.69 0.64 0.74 293 1108909 137 18 85 34 164
CRW_00096 0.75 0.68 0.81 318 1178489 108 6 67 35 147
CRW_00140 0.76 0.71 0.81 328 1135874 114 12 64 38 135
CRW_00141 0.69 0.64 0.75 305 1201619 132 14 87 31 171
CRW_00150 0.72 0.65 0.80 303 1152540 113 14 64 35 163
CRW_00152 0.76 0.70 0.82 332 1180009 110 11 64 35 139
CRW_00166 0.65 0.60 0.71 281 1190800 160 10 105 45 187
CRW_00173 0.57 0.52 0.63 232 1082285 168 19 120 29 213
CRW_00177 0.62 0.56 0.68 264 1178492 152 16 108 28 209
CRW_00196 0.73 0.67 0.80 319 1207837 117 10 69 38 156
CRW_00230 0.73 0.67 0.80 319 1198526 122 12 69 41 159
CRW_00245 0.73 0.67 0.81 302 1105955 106 13 58 35 151
CRW_00248 0.71 0.65 0.77 317 1218729 129 13 82 34 167
CRW_00250 0.73 0.67 0.79 321 1198521 119 12 72 35 157
CRW_00256 0.70 0.64 0.77 299 1192353 124 11 77 36 169
CRW_00270 0.72 0.67 0.77 306 1111891 121 14 75 32 149
CRW_00271 0.70 0.65 0.77 298 1122364 122 17 72 33 164
CRW_00273 0.68 0.62 0.74 277 1085225 135 13 86 36 169
CRW_00275 0.71 0.63 0.80 289 1114908 114 13 61 40 168
CRW_00277 0.68 0.63 0.73 286 1110405 132 17 87 28 167
CRW_00278 0.71 0.62 0.80 280 1129906 107 12 58 37 170
CRW_00279 0.70 0.64 0.77 299 1180027 133 10 80 43 165
CRW_00280 0.72 0.66 0.78 301 1117875 125 10 74 41 152
CRW_00281 0.71 0.65 0.78 303 1144954 117 13 71 33 161
CRW_00284 0.69 0.62 0.77 281 1131397 117 9 73 35 175
CRW_00285 0.70 0.64 0.77 292 1117883 123 15 70 38 166
CRW_00289 0.62 0.58 0.66 274 1189239 172 18 122 32 202
CRW_00298 0.48 0.46 0.51 226 1620454 284 45 175 64 268
CRW_00301 0.42 0.39 0.45 204 1762046 308 49 204 55 315
CRW_00306 0.43 0.40 0.46 183 1445453 276 47 167 62 279
CRW_00310 0.45 0.41 0.49 212 1805516 285 39 183 63 309
CRW_00326 0.49 0.45 0.53 227 1627679 267 35 169 63 275
CRW_00330 0.41 0.37 0.45 190 1988597 294 32 196 66 327
CRW_00332 0.37 0.34 0.40 163 1769615 307 47 196 64 314
CRW_00333 0.31 0.26 0.35 136 1892099 328 47 203 78 378
CRW_00345 0.46 0.44 0.49 219 1586422 293 53 177 63 279
CRW_00346 0.49 0.46 0.52 229 1584649 269 43 169 57 272
CRW_00348 0.49 0.47 0.52 235 1615052 277 51 165 61 268
CRW_00358 0.48 0.44 0.53 224 1674941 262 38 162 62 283
CRW_00366 0.42 0.40 0.43 195 1579299 332 47 212 73 287
CRW_00370 0.50 0.48 0.52 242 1640302 281 47 175 59 264
CRW_00371 0.49 0.46 0.53 229 1611474 266 39 168 59 267
CRW_00372 0.51 0.47 0.54 236 1625872 273 37 161 75 262
CRW_00379 0.37 0.33 0.42 175 2126532 323 40 206 77 359
CRW_00386 0.47 0.43 0.50 223 1750812 281 44 177 60 292
CRW_00403 0.45 0.41 0.48 192 1606131 304 37 168 99 272
CRW_00411 0.49 0.46 0.52 227 1615066 271 42 168 61 269
CRW_00414 0.39 0.37 0.41 181 1665782 316 50 212 54 314
CRW_00466 0.63 0.58 0.69 266 1116382 147 16 101 30 192
CRW_00589 0.69 0.62 0.76 277 1094097 130 6 80 44 168
CRW_00590 0.72 0.67 0.78 303 1119366 134 11 76 47 149
CRW_00591 0.74 0.68 0.81 303 1098531 115 7 62 46 143
CRW_00598 0.49 0.46 0.52 226 1665793 276 41 165 70 265
CRW_00758 0.46 0.43 0.48 207 1640338 292 44 177 71 276
CRW_00759 0.42 0.40 0.44 191 1636712 314 43 199 72 290
CRW_00760 0.46 0.43 0.49 208 1638533 291 37 177 77 278
CRW_00772 0.60 0.54 0.67 217 945677 148 10 96 42 187
CRW_00789 0.67 0.60 0.75 268 1137427 134 8 83 43 179
CRW_00795 0.63 0.57 0.71 224 1152605 176 10 82 84 170
CRW_00849 0.61 0.55 0.68 260 1117878 154 17 105 32 210
CRW_00997 0.74 0.69 0.79 322 1135872 121 12 72 37 142
CRW_01153 0.44 0.42 0.46 211 1606072 295 46 199 50 292
CRW_01171 0.48 0.45 0.51 229 1593556 274 47 173 54 277
CRW_01300 0.47 0.45 0.50 230 1693258 286 45 187 54 285
PDB_00703 0.69 0.60 0.79 295 1073472 114 10 68 36 200
PDB_00854 0.62 0.51 0.75 274 1500415 142 2 87 53 261
PDB_01088 0.66 0.56 0.78 308 1471077 135 7 78 50 239
PDB_01103 0.61 0.52 0.71 293 1606118 156 16 101 39 269
PDB_01105 0.64 0.54 0.75 291 1433583 134 3 94 37 249
PDB_01120 0.66 0.57 0.76 302 1204732 134 11 83 40 225
PDB_01273 0.69 0.60 0.79 294 1117886 120 10 70 40 197

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