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Table of contents:

  1. Overview

  2. Performance Plots

  3. Performance of PETfold_pre2.0(20) - scored higher in this pairwise comparison

  4. Performance of MXScarna(20) - scored lower in this pairwise comparison

  5. Compile and download dataset for PETfold_pre2.0(20) & MXScarna(20) [.zip] - may take several seconds...


Overview

Metric PETfold_pre2.0(20) MXScarna(20)
MCC 0.728 > 0.598
Average MCC ± 95% Confidence Intervals 0.730 ± 0.030 > 0.603 ± 0.029
Sensitivity 0.697 > 0.548
Positive Predictive Value 0.760 > 0.653
Total TP 25763 > 20251
Total TN 104336584 < 104339447
Total FP 11045 < 14477
Total FP CONTRA 1367 < 1798
Total FP INCONS 6752 < 8970
Total FP COMP 2926 < 3709
Total FN 11201 < 16713
P-value 3.56938820447e-08

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Performance plots


  1. Comparison of performance of PETfold_pre2.0(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 PETfold_pre2.0(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 PETfold_pre2.0(20) and MXScarna(20)).

  3. Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(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 PETfold_pre2.0(20) and MXScarna(20)).

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Performance of PETfold_pre2.0(20) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(20)

Total Base Pair Counts
Total TP 25763
Total TN 104336584
Total FP 11045
Total FP CONTRA 1367
Total FP INCONS 6752
Total FP COMP 2926
Total FN 11201
Total Scores
MCC 0.728
Average MCC ± 95% Confidence Intervals 0.730 ± 0.030
Sensitivity 0.697
Positive Predictive Value 0.760
Nr of predictions 77

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2. Individual counts for PETfold_pre2.0(20) [ download as .csv ]

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.89 0.88 0.90 404 1085151 82 10 36 36 54
CRW_00034 0.82 0.79 0.85 374 1141875 86 17 50 19 100
CRW_00048 0.84 0.83 0.84 390 1170753 91 18 54 19 80
CRW_00054 0.84 0.84 0.84 381 1107361 95 17 57 21 75
CRW_00059 0.84 0.82 0.85 390 1172289 85 17 50 18 83
CRW_00061 0.84 0.82 0.86 390 1181501 85 16 46 23 86
CRW_00068 0.84 0.84 0.84 383 1108851 87 16 55 16 74
CRW_00096 0.85 0.83 0.87 388 1178436 81 12 44 25 77
CRW_00140 0.85 0.84 0.86 388 1135827 85 15 48 22 75
CRW_00141 0.83 0.81 0.85 387 1201568 90 18 52 20 89
CRW_00150 0.83 0.82 0.85 381 1152473 90 16 51 23 85
CRW_00152 0.83 0.81 0.85 381 1179968 89 17 50 22 90
CRW_00166 0.85 0.83 0.86 387 1190748 90 11 50 29 81
CRW_00173 0.80 0.80 0.81 354 1082220 107 18 64 25 91
CRW_00177 0.82 0.81 0.84 382 1178424 101 17 57 27 91
CRW_00196 0.83 0.81 0.85 387 1207780 91 16 52 23 88
CRW_00230 0.85 0.82 0.87 394 1198472 81 16 44 21 84
CRW_00245 0.87 0.86 0.87 390 1105881 79 17 40 22 63
CRW_00248 0.84 0.82 0.87 396 1218684 87 15 46 26 88
CRW_00250 0.83 0.80 0.85 382 1198478 88 15 51 22 96
CRW_00256 0.83 0.81 0.85 379 1192296 87 16 49 22 89
CRW_00270 0.86 0.86 0.86 390 1111833 85 15 48 22 65
CRW_00271 0.82 0.81 0.84 375 1122302 98 14 60 24 87
CRW_00273 0.84 0.84 0.84 375 1085156 94 14 56 24 71
CRW_00275 0.86 0.86 0.87 391 1114821 86 15 44 27 66
CRW_00277 0.84 0.84 0.85 379 1110348 89 16 52 21 74
CRW_00278 0.84 0.82 0.86 371 1129827 85 12 46 27 79
CRW_00279 0.82 0.81 0.84 377 1179965 98 18 56 24 87
CRW_00280 0.85 0.85 0.86 384 1117811 93 15 50 28 69
CRW_00281 0.84 0.82 0.85 381 1144895 89 14 51 24 83
CRW_00284 0.84 0.82 0.85 376 1131317 94 16 51 27 80
CRW_00285 0.84 0.83 0.86 380 1117816 91 17 47 27 78
CRW_00289 0.83 0.81 0.85 386 1189199 95 13 55 27 90
CRW_00298 0.58 0.54 0.63 267 1620473 212 31 129 52 227
CRW_00301 0.49 0.46 0.53 240 1762048 265 37 178 50 279
CRW_00306 0.60 0.57 0.63 263 1445430 208 26 131 51 199
CRW_00310 0.55 0.51 0.59 264 1805500 238 32 154 52 257
CRW_00326 0.64 0.60 0.68 299 1627669 193 22 120 51 203
CRW_00330 0.55 0.51 0.60 262 1988577 231 26 150 55 255
CRW_00332 0.51 0.48 0.56 227 1769613 237 20 161 56 250
CRW_00333 0.48 0.43 0.53 220 1892069 260 36 160 64 294
CRW_00345 0.56 0.53 0.60 262 1586434 224 28 147 49 236
CRW_00346 0.59 0.55 0.63 278 1584648 213 32 132 49 223
CRW_00348 0.58 0.54 0.61 272 1615059 225 29 143 53 231
CRW_00358 0.56 0.53 0.60 269 1674914 228 29 153 46 238
CRW_00366 0.60 0.56 0.64 269 1579331 210 25 128 57 213
CRW_00370 0.60 0.57 0.64 288 1640315 211 20 143 48 218
CRW_00371 0.58 0.55 0.60 275 1611455 232 17 163 52 221
CRW_00372 0.59 0.55 0.62 275 1625865 212 23 143 46 223
CRW_00379 0.58 0.52 0.65 277 2126526 213 25 125 63 257
CRW_00386 0.49 0.46 0.53 236 1750812 258 28 180 50 279
CRW_00403 0.53 0.52 0.54 240 1606084 283 31 173 79 224
CRW_00411 0.58 0.54 0.61 269 1615064 222 21 149 52 227
CRW_00414 0.57 0.53 0.62 263 1665801 210 25 136 49 232
CRW_00466 0.85 0.85 0.85 388 1116310 90 13 54 23 70
CRW_00589 0.84 0.82 0.86 367 1094034 98 8 51 39 78
CRW_00590 0.87 0.84 0.89 381 1119329 87 4 42 41 71
CRW_00591 0.85 0.84 0.86 373 1098469 103 7 54 42 73
CRW_00598 0.54 0.51 0.58 250 1665793 234 28 154 52 241
CRW_00758 0.57 0.54 0.61 263 1640333 241 27 143 71 220
CRW_00759 0.56 0.53 0.59 254 1636715 232 18 158 56 227
CRW_00760 0.53 0.49 0.57 239 1638533 247 16 167 64 247
CRW_00772 0.78 0.76 0.80 306 945618 127 7 69 51 98
CRW_00789 0.82 0.80 0.85 357 1137365 108 8 56 44 90
CRW_00795 0.79 0.76 0.82 301 1152552 149 5 63 81 93
CRW_00849 0.80 0.78 0.82 366 1117816 101 14 64 23 104
CRW_00997 0.85 0.84 0.85 389 1135822 85 16 51 18 75
CRW_01153 0.59 0.56 0.63 283 1606076 220 25 144 51 220
CRW_01171 0.52 0.48 0.56 245 1593566 240 31 163 46 261
CRW_01300 0.60 0.55 0.67 283 1693295 193 17 125 51 232
PDB_00703 0.78 0.72 0.84 355 1073423 101 6 61 34 140
PDB_00854 0.75 0.68 0.84 363 1500344 118 10 61 47 172
PDB_01088 0.74 0.65 0.83 357 1471042 115 5 66 44 190
PDB_01103 0.75 0.66 0.85 373 1606088 99 8 59 32 189
PDB_01105 0.75 0.68 0.84 366 1433533 107 4 68 35 174
PDB_01120 0.78 0.72 0.85 378 1204681 101 9 60 32 149
PDB_01273 0.78 0.73 0.84 358 1117834 110 9 59 42 133

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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.