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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 Sfold - scored lower in this pairwise comparison

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


Overview

Metric PETfold_pre2.0(20) Sfold
MCC 0.728 > 0.453
Average MCC ± 95% Confidence Intervals 0.730 ± 0.030 > 0.455 ± 0.031
Sensitivity 0.697 > 0.403
Positive Predictive Value 0.760 > 0.510
Total TP 25763 > 14880
Total TN 104336584 < 104341300
Total FP 11045 < 16483
Total FP CONTRA 1367 < 2320
Total FP INCONS 6752 < 11966
Total FP COMP 2926 > 2197
Total FN 11201 < 22084
P-value 3.56938820447e-08

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Performance plots


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

  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 Sfold).

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

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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 Sfold - scored lower in this pairwise comparison

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP 14880
Total TN 104341300
Total FP 16483
Total FP CONTRA 2320
Total FP INCONS 11966
Total FP COMP 2197
Total FN 22084
Total Scores
MCC 0.453
Average MCC ± 95% Confidence Intervals 0.455 ± 0.031
Sensitivity 0.403
Positive Predictive Value 0.510
Nr of predictions 77

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.80 0.77 0.83 352 1085176 112 13 60 39 106
CRW_00034 0.65 0.64 0.66 304 1141856 180 27 129 24 170
CRW_00048 0.50 0.45 0.54 213 1170824 198 17 161 20 257
CRW_00054 0.48 0.43 0.54 195 1107453 185 23 145 17 261
CRW_00059 0.54 0.49 0.60 232 1172361 169 19 134 16 241
CRW_00061 0.49 0.45 0.54 215 1181555 193 31 152 10 261
CRW_00068 0.48 0.43 0.53 196 1108938 184 19 152 13 261
CRW_00096 0.59 0.55 0.63 258 1178469 180 16 137 27 207
CRW_00140 0.66 0.60 0.73 280 1135893 125 10 95 20 183
CRW_00141 0.63 0.57 0.70 272 1201636 139 16 101 22 204
CRW_00150 0.40 0.37 0.44 171 1152531 233 30 189 14 295
CRW_00152 0.67 0.61 0.74 287 1180029 118 21 79 18 184
CRW_00166 0.54 0.47 0.61 221 1190832 160 15 128 17 247
CRW_00173 0.36 0.32 0.39 144 1082291 233 16 205 12 301
CRW_00177 0.45 0.41 0.50 195 1178491 206 27 167 12 278
CRW_00196 0.47 0.44 0.50 210 1207811 232 23 191 18 265
CRW_00230 0.61 0.53 0.70 254 1198565 129 7 100 22 224
CRW_00245 0.54 0.45 0.66 202 1106023 115 16 87 12 251
CRW_00248 0.58 0.57 0.59 274 1218677 223 21 169 33 210
CRW_00250 0.50 0.46 0.54 221 1198516 206 28 161 17 257
CRW_00256 0.37 0.33 0.42 155 1192370 232 35 180 17 313
CRW_00270 0.48 0.39 0.59 178 1111985 137 19 104 14 277
CRW_00271 0.49 0.43 0.57 198 1122402 170 32 119 19 264
CRW_00273 0.55 0.50 0.61 224 1085232 162 22 123 17 222
CRW_00275 0.58 0.47 0.73 213 1114978 98 14 66 18 244
CRW_00277 0.40 0.30 0.54 136 1110544 127 18 97 12 317
CRW_00278 0.51 0.37 0.70 166 1130018 88 6 66 16 284
CRW_00279 0.61 0.54 0.69 252 1180052 131 20 92 19 212
CRW_00280 0.60 0.55 0.66 250 1117881 149 21 108 20 203
CRW_00281 0.68 0.60 0.77 279 1144977 109 11 74 24 185
CRW_00284 0.42 0.33 0.53 149 1131480 147 20 111 16 307
CRW_00285 0.77 0.71 0.83 326 1117866 94 16 52 26 132
CRW_00289 0.59 0.51 0.68 241 1189298 141 19 95 27 235
CRW_00298 0.19 0.17 0.21 84 1620496 355 58 262 35 410
CRW_00301 0.33 0.30 0.36 156 1762064 326 45 238 43 363
CRW_00306 0.21 0.19 0.24 88 1445476 332 57 229 46 374
CRW_00310 0.30 0.26 0.35 138 1805554 298 56 202 40 383
CRW_00326 0.46 0.37 0.56 187 1627778 175 32 113 30 315
CRW_00330 0.34 0.28 0.41 145 1988661 279 50 159 70 372
CRW_00332 0.22 0.21 0.24 102 1769589 370 75 255 40 375
CRW_00333 0.30 0.30 0.31 153 1891989 400 68 275 57 361
CRW_00345 0.40 0.35 0.45 173 1586487 244 36 175 33 325
CRW_00346 0.34 0.32 0.36 161 1584648 319 58 223 38 340
CRW_00348 0.32 0.26 0.40 129 1615184 223 34 156 33 374
CRW_00358 0.38 0.33 0.43 166 1674980 241 44 175 22 341
CRW_00366 0.36 0.35 0.36 169 1579286 334 74 224 36 313
CRW_00370 0.34 0.32 0.36 160 1640327 325 54 225 46 346
CRW_00371 0.38 0.34 0.42 171 1611504 271 50 185 36 325
CRW_00372 0.39 0.35 0.45 172 1625925 245 34 175 36 326
CRW_00379 0.44 0.34 0.58 183 2126636 205 17 117 71 351
CRW_00386 0.29 0.27 0.31 138 1750806 345 60 252 33 377
CRW_00403 0.31 0.30 0.32 137 1606104 362 58 229 75 327
CRW_00411 0.39 0.32 0.47 157 1615171 217 28 147 42 339
CRW_00414 0.33 0.29 0.38 146 1665840 278 40 199 39 349
CRW_00466 0.57 0.54 0.61 247 1116358 185 18 142 25 211
CRW_00589 0.31 0.26 0.36 116 1094139 220 19 186 15 329
CRW_00590 0.58 0.40 0.84 179 1119542 50 5 30 15 273
CRW_00591 0.60 0.56 0.65 248 1098523 153 22 110 21 198
CRW_00598 0.35 0.34 0.37 165 1665773 333 62 225 46 326
CRW_00758 0.34 0.30 0.38 147 1640380 287 42 197 48 336
CRW_00759 0.23 0.22 0.25 105 1636722 354 42 276 36 376
CRW_00760 0.33 0.27 0.39 133 1638613 257 32 177 48 353
CRW_00772 0.30 0.27 0.34 108 945681 233 27 184 22 296
CRW_00789 0.40 0.34 0.46 152 1137458 193 30 146 17 295
CRW_00795 0.19 0.17 0.20 68 1152586 311 44 223 44 326
CRW_00849 0.50 0.48 0.52 227 1117826 230 18 189 23 243
CRW_00997 0.59 0.52 0.66 241 1135913 144 19 105 20 223
CRW_01153 0.37 0.30 0.45 152 1606193 221 35 148 38 351
CRW_01171 0.33 0.29 0.38 149 1593608 285 55 193 37 357
CRW_01300 0.39 0.34 0.45 175 1693327 254 42 176 36 340
PDB_00703 0.52 0.46 0.58 229 1073451 189 12 153 24 266
PDB_00854 0.54 0.49 0.60 263 1500337 220 22 156 42 272
PDB_01088 0.38 0.32 0.47 173 1471098 222 33 166 23 374
PDB_01103 0.56 0.50 0.63 280 1606082 191 20 146 25 282
PDB_01105 0.60 0.53 0.67 288 1433540 169 14 129 26 252
PDB_01120 0.55 0.44 0.70 230 1204799 110 12 87 11 297
PDB_01273 0.50 0.46 0.54 227 1117836 223 19 178 26 264

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