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Table of contents:

  1. Overview

  2. Performance Plots

  3. Performance of PETfold_pre2.0(seed) - 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(seed) & MXScarna(20) [.zip] - may take several seconds...


Overview

Metric PETfold_pre2.0(seed) MXScarna(20)
MCC 0.760 > 0.598
Average MCC ± 95% Confidence Intervals 0.763 ± 0.022 > 0.603 ± 0.029
Sensitivity 0.730 > 0.548
Positive Predictive Value 0.792 > 0.653
Total TP 26994 > 20251
Total TN 104336380 < 104339447
Total FP 11076 < 14477
Total FP CONTRA 1094 < 1798
Total FP INCONS 5998 < 8970
Total FP COMP 3984 > 3709
Total FN 9970 < 16713
P-value 3.56938820447e-08

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Performance plots


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

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

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

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

Total Base Pair Counts
Total TP 26994
Total TN 104336380
Total FP 11076
Total FP CONTRA 1094
Total FP INCONS 5998
Total FP COMP 3984
Total FN 9970
Total Scores
MCC 0.760
Average MCC ± 95% Confidence Intervals 0.763 ± 0.022
Sensitivity 0.730
Positive Predictive Value 0.792
Nr of predictions 77

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2. Individual counts for PETfold_pre2.0(seed) [ 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 0.90 405 1085153 80 10 33 37 53
CRW_00034 0.80 0.78 0.83 369 1141870 113 17 60 36 105
CRW_00048 0.85 0.84 0.87 395 1170759 96 18 43 35 75
CRW_00054 0.86 0.86 0.87 390 1107367 95 16 43 36 66
CRW_00059 0.85 0.83 0.87 392 1172293 95 17 44 34 81
CRW_00061 0.84 0.82 0.86 388 1181504 96 16 45 35 88
CRW_00068 0.86 0.86 0.87 394 1108851 94 17 43 34 63
CRW_00096 0.86 0.84 0.88 392 1178434 98 11 43 44 73
CRW_00140 0.85 0.84 0.86 387 1135829 97 15 47 35 76
CRW_00141 0.85 0.82 0.87 392 1201573 98 16 44 38 84
CRW_00150 0.85 0.83 0.87 385 1152477 92 16 43 33 81
CRW_00152 0.84 0.82 0.86 386 1179969 96 16 45 35 85
CRW_00166 0.86 0.84 0.88 393 1190749 97 11 43 43 75
CRW_00173 0.80 0.79 0.81 353 1082222 118 17 64 37 92
CRW_00177 0.84 0.82 0.86 386 1178430 105 17 47 41 87
CRW_00196 0.83 0.81 0.86 384 1207786 102 15 50 37 91
CRW_00230 0.84 0.82 0.87 392 1198473 97 16 45 36 86
CRW_00245 0.86 0.86 0.87 388 1105880 95 18 42 35 65
CRW_00248 0.83 0.80 0.86 388 1218691 98 16 46 36 96
CRW_00250 0.84 0.82 0.87 391 1198474 97 16 45 36 87
CRW_00256 0.85 0.82 0.87 386 1192295 93 16 43 34 82
CRW_00270 0.87 0.86 0.87 391 1111838 94 15 42 37 64
CRW_00271 0.83 0.82 0.85 378 1122307 105 14 52 39 84
CRW_00273 0.86 0.85 0.86 380 1085161 98 14 46 38 66
CRW_00275 0.86 0.85 0.87 390 1114823 98 15 43 40 67
CRW_00277 0.84 0.83 0.85 377 1110354 101 16 48 37 76
CRW_00278 0.84 0.82 0.85 369 1129823 106 15 49 42 81
CRW_00279 0.85 0.83 0.86 385 1179970 103 16 45 42 79
CRW_00280 0.84 0.83 0.85 377 1117815 109 16 52 41 76
CRW_00281 0.85 0.84 0.87 388 1144894 97 16 43 38 76
CRW_00284 0.83 0.82 0.84 372 1131319 111 16 53 42 84
CRW_00285 0.84 0.82 0.85 377 1117816 104 17 50 37 81
CRW_00289 0.82 0.80 0.84 382 1189200 109 16 55 38 94
CRW_00298 0.66 0.63 0.69 310 1620452 212 16 122 74 184
CRW_00301 0.63 0.59 0.67 307 1762046 213 15 135 63 212
CRW_00306 0.68 0.66 0.70 305 1445417 186 15 113 58 157
CRW_00310 0.63 0.59 0.68 305 1805503 209 14 128 67 216
CRW_00326 0.66 0.63 0.69 315 1627654 205 15 126 64 187
CRW_00330 0.64 0.59 0.69 307 1988567 210 13 128 69 210
CRW_00332 0.60 0.56 0.63 269 1769595 236 16 141 79 208
CRW_00333 0.58 0.52 0.64 269 1892065 217 19 132 66 245
CRW_00345 0.64 0.61 0.67 305 1586418 211 15 133 63 193
CRW_00346 0.65 0.61 0.69 308 1584644 204 15 123 66 193
CRW_00348 0.65 0.62 0.68 312 1615046 210 15 130 65 191
CRW_00358 0.64 0.60 0.67 306 1674911 213 16 132 65 201
CRW_00366 0.65 0.62 0.68 300 1579311 211 15 127 69 182
CRW_00370 0.65 0.62 0.69 313 1640313 205 15 125 65 193
CRW_00371 0.68 0.65 0.71 322 1611455 199 13 120 66 174
CRW_00372 0.64 0.61 0.67 306 1625847 221 14 139 68 192
CRW_00379 0.60 0.54 0.66 286 2126521 223 18 128 77 248
CRW_00386 0.61 0.58 0.65 297 1750802 227 16 141 70 218
CRW_00403 0.68 0.66 0.70 306 1606090 215 15 117 83 158
CRW_00411 0.67 0.64 0.71 318 1615053 200 15 117 68 178
CRW_00414 0.64 0.61 0.67 303 1665770 223 20 132 71 192
CRW_00466 0.86 0.85 0.87 391 1116315 99 14 45 40 67
CRW_00589 0.87 0.84 0.89 376 1094037 99 6 41 52 69
CRW_00590 0.87 0.84 0.89 381 1119327 104 6 42 56 71
CRW_00591 0.87 0.86 0.89 382 1098473 103 6 42 55 64
CRW_00598 0.63 0.60 0.66 294 1665777 224 19 135 70 197
CRW_00758 0.64 0.61 0.67 294 1640327 224 15 130 79 189
CRW_00759 0.65 0.62 0.68 297 1636709 218 15 124 79 184
CRW_00760 0.63 0.59 0.66 287 1638522 227 17 129 81 199
CRW_00772 0.79 0.76 0.81 309 945618 130 6 67 57 95
CRW_00789 0.83 0.81 0.86 362 1137365 112 11 48 53 85
CRW_00795 0.79 0.76 0.82 299 1152557 159 6 59 94 95
CRW_00849 0.79 0.76 0.81 359 1117819 116 16 66 34 111
CRW_00997 0.86 0.85 0.87 395 1135823 93 17 43 33 69
CRW_01153 0.61 0.58 0.64 294 1606070 223 18 146 59 209
CRW_01171 0.63 0.60 0.67 304 1593548 214 15 138 61 202
CRW_01300 0.62 0.59 0.66 302 1693261 218 17 140 61 213
PDB_00703 0.79 0.73 0.86 361 1073423 107 9 52 46 134
PDB_00854 0.76 0.68 0.86 364 1500354 120 9 51 60 171
PDB_01088 0.75 0.67 0.85 365 1471040 119 5 60 54 182
PDB_01103 0.76 0.67 0.86 376 1606090 108 8 54 46 186
PDB_01105 0.77 0.70 0.86 376 1433534 108 3 58 47 164
PDB_01120 0.80 0.73 0.86 387 1204680 102 10 51 41 140
PDB_01273 0.80 0.75 0.86 368 1117832 112 8 52 52 123

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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.