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Table of contents:

  1. Overview

  2. Performance Plots

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

  4. Performance of ProbKnot - scored lower in this pairwise comparison

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


Overview

Metric CentroidAlifold(20) ProbKnot
MCC 0.726 > 0.408
Average MCC ± 95% Confidence Intervals 0.718 ± 0.036 > 0.410 ± 0.026
Sensitivity 0.614 > 0.403
Positive Predictive Value 0.860 > 0.412
Total TP 22679 > 14903
Total TN 104344087 > 104334324
Total FP 5560 < 24166
Total FP CONTRA 629 < 3608
Total FP INCONS 3071 < 17631
Total FP COMP 1860 < 2927
Total FN 14285 < 22061
P-value 3.56938820447e-08

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Performance plots


  1. Comparison of performance of CentroidAlifold(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 CentroidAlifold(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 CentroidAlifold(20) and ProbKnot).

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

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Performance of CentroidAlifold(20) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP 22679
Total TN 104344087
Total FP 5560
Total FP CONTRA 629
Total FP INCONS 3071
Total FP COMP 1860
Total FN 14285
Total Scores
MCC 0.726
Average MCC ± 95% Confidence Intervals 0.718 ± 0.036
Sensitivity 0.614
Positive Predictive Value 0.860
Nr of predictions 77

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.91 0.86 0.95 394 1085188 51 6 13 32 64
CRW_00034 0.83 0.77 0.90 365 1141911 54 9 31 14 109
CRW_00048 0.86 0.80 0.93 374 1170812 45 10 19 16 96
CRW_00054 0.86 0.80 0.93 364 1107423 43 10 19 14 92
CRW_00059 0.85 0.78 0.93 368 1172351 42 9 18 15 105
CRW_00061 0.86 0.80 0.92 380 1181542 47 10 21 16 96
CRW_00068 0.85 0.80 0.91 365 1108906 48 11 23 14 92
CRW_00096 0.86 0.78 0.95 363 1178497 43 4 16 23 102
CRW_00140 0.86 0.80 0.92 372 1135875 46 11 20 15 91
CRW_00141 0.85 0.78 0.93 371 1201625 47 10 19 18 105
CRW_00150 0.86 0.80 0.92 372 1152515 48 10 24 14 94
CRW_00152 0.84 0.77 0.91 364 1180015 52 13 24 15 107
CRW_00166 0.86 0.78 0.94 364 1190809 45 4 19 22 104
CRW_00173 0.80 0.75 0.86 332 1082272 67 11 41 15 113
CRW_00177 0.83 0.75 0.92 356 1178493 48 7 24 17 117
CRW_00196 0.86 0.79 0.94 377 1207832 45 8 18 19 98
CRW_00230 0.86 0.79 0.94 378 1198524 39 8 16 15 100
CRW_00245 0.87 0.81 0.93 367 1105932 46 9 20 17 86
CRW_00248 0.85 0.77 0.92 375 1218735 46 11 20 15 109
CRW_00250 0.84 0.77 0.92 370 1198524 46 11 21 14 108
CRW_00256 0.84 0.77 0.91 360 1192345 51 10 25 16 108
CRW_00270 0.86 0.80 0.92 362 1111893 46 11 20 15 93
CRW_00271 0.84 0.77 0.91 355 1122363 48 8 25 15 107
CRW_00273 0.86 0.79 0.92 354 1085218 46 8 21 17 92
CRW_00275 0.87 0.81 0.93 371 1114870 46 9 21 16 86
CRW_00277 0.85 0.78 0.91 354 1110408 50 12 21 17 99
CRW_00278 0.84 0.78 0.91 351 1129869 54 7 29 18 99
CRW_00279 0.84 0.77 0.92 357 1180030 50 8 21 21 107
CRW_00280 0.84 0.79 0.89 357 1117860 63 9 34 20 96
CRW_00281 0.84 0.77 0.92 357 1144951 49 9 24 16 107
CRW_00284 0.84 0.77 0.91 350 1131377 50 7 26 17 106
CRW_00285 0.83 0.77 0.90 353 1117869 56 11 27 18 105
CRW_00289 0.82 0.75 0.91 356 1189260 53 9 28 16 120
CRW_00298 0.52 0.37 0.72 183 1620647 90 6 64 20 311
CRW_00301 0.47 0.34 0.64 178 1762223 133 11 91 31 341
CRW_00306 0.52 0.37 0.73 171 1445616 97 6 57 34 291
CRW_00310 0.49 0.37 0.66 192 1805657 126 13 88 25 329
CRW_00326 0.57 0.40 0.80 201 1627859 78 6 44 28 301
CRW_00330 0.51 0.37 0.71 190 1988747 113 10 68 35 327
CRW_00332 0.48 0.34 0.67 161 1769781 123 8 71 44 316
CRW_00333 0.43 0.30 0.61 155 1892229 131 20 81 30 359
CRW_00345 0.51 0.36 0.72 181 1586621 96 8 61 27 317
CRW_00346 0.53 0.38 0.74 192 1584829 102 6 63 33 309
CRW_00348 0.54 0.40 0.72 200 1615226 107 10 67 30 303
CRW_00358 0.53 0.39 0.73 196 1675098 99 8 63 28 311
CRW_00366 0.52 0.37 0.71 180 1579501 100 8 64 28 302
CRW_00370 0.58 0.41 0.83 208 1640515 64 4 39 21 298
CRW_00371 0.55 0.40 0.75 199 1611646 93 8 57 28 297
CRW_00372 0.50 0.37 0.69 182 1626042 112 11 71 30 316
CRW_00379 0.49 0.33 0.72 176 2126710 109 5 62 42 358
CRW_00386 0.51 0.35 0.73 182 1751006 96 7 61 28 333
CRW_00403 0.52 0.39 0.70 180 1606270 126 11 67 48 284
CRW_00411 0.51 0.38 0.68 189 1615224 117 8 82 27 307
CRW_00414 0.48 0.34 0.67 170 1665972 109 11 72 26 325
CRW_00466 0.86 0.79 0.93 364 1116372 45 9 20 16 94
CRW_00589 0.86 0.78 0.94 347 1094091 45 2 20 23 98
CRW_00590 0.86 0.79 0.93 359 1119369 53 3 25 25 93
CRW_00591 0.86 0.79 0.92 354 1098520 55 6 23 26 92
CRW_00598 0.49 0.34 0.70 169 1665982 103 5 69 29 322
CRW_00758 0.52 0.38 0.72 184 1640510 108 6 66 36 299
CRW_00759 0.51 0.38 0.69 181 1636884 113 8 72 33 300
CRW_00760 0.52 0.37 0.74 180 1638713 102 7 55 40 306
CRW_00772 0.79 0.73 0.85 295 945652 81 5 48 28 109
CRW_00789 0.83 0.76 0.91 340 1137411 63 5 30 28 107
CRW_00795 0.80 0.72 0.88 284 1152598 97 3 36 58 110
CRW_00849 0.82 0.76 0.88 357 1117854 65 10 39 16 113
CRW_00997 0.85 0.80 0.91 369 1135873 50 13 23 14 95
CRW_01153 0.50 0.36 0.69 179 1606270 108 8 71 29 324
CRW_01171 0.49 0.36 0.67 183 1593733 116 11 78 27 323
CRW_01300 0.55 0.40 0.76 205 1693451 88 6 58 24 310
PDB_00703 0.81 0.70 0.92 348 1073468 55 8 21 26 147
PDB_00854 0.77 0.65 0.90 348 1500393 73 4 33 36 187
PDB_01088 0.75 0.62 0.90 341 1471090 76 2 37 37 206
PDB_01103 0.77 0.64 0.92 361 1606134 59 8 25 26 201
PDB_01105 0.78 0.66 0.92 359 1433581 59 2 29 28 181
PDB_01120 0.79 0.68 0.92 357 1204739 53 7 25 21 170
PDB_01273 0.80 0.69 0.91 341 1117886 62 6 27 29 150

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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.