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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 ProbKnot - scored lower in this pairwise comparison

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


Overview

Metric PETfold_pre2.0(20) ProbKnot
MCC 0.728 > 0.408
Average MCC ± 95% Confidence Intervals 0.730 ± 0.030 > 0.410 ± 0.026
Sensitivity 0.697 > 0.403
Positive Predictive Value 0.760 > 0.412
Total TP 25763 > 14903
Total TN 104336584 > 104334324
Total FP 11045 < 24166
Total FP CONTRA 1367 < 3608
Total FP INCONS 6752 < 17631
Total FP COMP 2926 < 2927
Total FN 11201 < 22061
P-value 3.56938820447e-08

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Performance plots


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

  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 ProbKnot).

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

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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 ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP 14903
Total TN 104334324
Total FP 24166
Total FP CONTRA 3608
Total FP INCONS 17631
Total FP COMP 2927
Total FN 22061
Total Scores
MCC 0.408
Average MCC ± 95% Confidence Intervals 0.410 ± 0.026
Sensitivity 0.403
Positive Predictive Value 0.412
Nr of predictions 77

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.69 0.68 0.70 312 1085154 184 22 113 49 146
CRW_00034 0.65 0.64 0.66 305 1141852 193 33 126 34 169
CRW_00048 0.48 0.46 0.51 215 1170796 225 31 173 21 255
CRW_00054 0.42 0.41 0.43 186 1107383 267 27 220 20 270
CRW_00059 0.50 0.48 0.52 225 1172311 230 27 183 20 248
CRW_00061 0.43 0.42 0.44 201 1181493 284 39 220 25 275
CRW_00068 0.45 0.43 0.47 198 1108880 243 33 194 16 259
CRW_00096 0.49 0.48 0.50 222 1178435 246 25 198 23 243
CRW_00140 0.41 0.40 0.41 185 1135829 286 31 233 22 278
CRW_00141 0.54 0.52 0.55 248 1201576 229 30 171 28 228
CRW_00150 0.44 0.42 0.45 198 1152481 263 27 215 21 268
CRW_00152 0.58 0.56 0.60 265 1179971 202 39 141 22 206
CRW_00166 0.42 0.41 0.44 190 1190764 263 30 212 21 278
CRW_00173 0.27 0.26 0.27 115 1082237 320 30 274 16 330
CRW_00177 0.48 0.46 0.51 219 1178447 241 25 189 27 254
CRW_00196 0.49 0.48 0.50 229 1207778 250 33 195 22 246
CRW_00230 0.56 0.53 0.59 255 1198497 206 24 150 32 223
CRW_00245 0.40 0.40 0.41 179 1105891 278 32 226 20 274
CRW_00248 0.52 0.52 0.53 250 1218666 257 31 194 32 234
CRW_00250 0.50 0.50 0.50 238 1198447 265 46 195 24 240
CRW_00256 0.40 0.40 0.41 185 1192284 296 39 232 25 283
CRW_00270 0.53 0.53 0.54 241 1111840 228 28 177 23 214
CRW_00271 0.35 0.33 0.36 154 1122325 292 38 234 20 308
CRW_00273 0.43 0.41 0.45 183 1085197 235 32 189 14 263
CRW_00275 0.60 0.58 0.61 266 1114835 193 26 144 23 191
CRW_00277 0.36 0.35 0.37 157 1110374 282 40 224 18 296
CRW_00278 0.38 0.36 0.40 162 1129847 266 32 215 19 288
CRW_00279 0.54 0.52 0.57 243 1179987 211 33 153 25 221
CRW_00280 0.36 0.35 0.38 158 1117841 277 40 221 16 295
CRW_00281 0.58 0.56 0.59 260 1144904 208 25 152 31 204
CRW_00284 0.37 0.35 0.40 159 1131362 267 28 211 28 297
CRW_00285 0.55 0.53 0.56 244 1117827 214 31 158 25 214
CRW_00289 0.49 0.48 0.50 228 1189195 264 43 187 34 248
CRW_00298 0.23 0.24 0.22 119 1620359 466 89 333 44 375
CRW_00301 0.33 0.34 0.33 177 1761960 439 71 295 73 342
CRW_00306 0.18 0.19 0.18 86 1445359 473 69 336 68 376
CRW_00310 0.30 0.31 0.29 160 1805396 450 77 317 56 361
CRW_00326 0.40 0.41 0.40 207 1627588 371 65 250 56 295
CRW_00330 0.33 0.34 0.31 178 1988449 473 80 308 85 339
CRW_00332 0.18 0.19 0.17 90 1769489 491 93 349 49 387
CRW_00333 0.31 0.31 0.31 157 1891971 430 72 285 73 357
CRW_00345 0.35 0.35 0.35 173 1586376 380 60 262 58 325
CRW_00346 0.37 0.38 0.37 188 1584581 368 66 255 47 313
CRW_00348 0.30 0.30 0.31 149 1615021 383 63 270 50 354
CRW_00358 0.40 0.40 0.39 202 1674852 365 59 252 54 305
CRW_00366 0.26 0.27 0.25 130 1579227 438 85 311 42 352
CRW_00370 0.29 0.30 0.28 150 1640234 427 81 301 45 356
CRW_00371 0.39 0.39 0.40 191 1611430 345 53 236 56 305
CRW_00372 0.27 0.27 0.26 136 1625786 435 79 305 51 362
CRW_00379 0.42 0.43 0.41 229 2126396 414 75 253 86 305
CRW_00386 0.26 0.27 0.25 138 1750696 459 82 340 37 377
CRW_00403 0.31 0.31 0.31 143 1606064 418 64 257 97 321
CRW_00411 0.34 0.35 0.33 172 1614983 394 81 267 46 324
CRW_00414 0.29 0.30 0.29 149 1665709 429 66 301 62 346
CRW_00466 0.60 0.59 0.60 272 1116312 211 33 148 30 186
CRW_00589 0.31 0.30 0.32 135 1094033 316 46 246 24 310
CRW_00590 0.41 0.39 0.43 176 1119350 259 29 201 29 276
CRW_00591 0.44 0.44 0.44 198 1098453 275 46 206 23 248
CRW_00598 0.37 0.38 0.35 186 1665698 397 77 264 56 305
CRW_00758 0.32 0.32 0.32 155 1640275 399 64 272 63 328
CRW_00759 0.31 0.31 0.30 151 1636639 423 69 286 68 330
CRW_00760 0.29 0.30 0.29 146 1638444 427 68 297 62 340
CRW_00772 0.22 0.22 0.22 90 945593 335 34 283 18 314
CRW_00789 0.36 0.36 0.37 163 1137340 312 43 240 29 284
CRW_00795 0.34 0.34 0.33 135 1152513 326 45 228 53 259
CRW_00849 0.57 0.56 0.58 263 1117810 226 18 169 39 207
CRW_00997 0.44 0.42 0.46 197 1135851 249 39 191 19 267
CRW_01153 0.29 0.30 0.28 150 1605991 434 63 324 47 353
CRW_01171 0.33 0.33 0.33 168 1593497 395 62 278 55 338
CRW_01300 0.35 0.35 0.36 182 1693209 381 68 261 52 333
PDB_00703 0.56 0.51 0.61 253 1073430 187 22 140 25 242
PDB_00854 0.56 0.54 0.58 288 1500280 260 33 177 50 247
PDB_01088 0.33 0.32 0.34 175 1470956 367 49 290 28 372
PDB_01103 0.61 0.58 0.64 324 1606022 220 26 156 38 238
PDB_01105 0.57 0.53 0.62 286 1433506 213 32 147 34 254
PDB_01120 0.43 0.40 0.47 211 1204677 265 29 211 25 316
PDB_01273 0.43 0.41 0.45 200 1117813 276 33 214 29 291

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