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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 CentroidAlifold(20) - scored lower in this pairwise comparison

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


Overview

Metric PETfold_pre2.0(20) CentroidAlifold(20)
MCC 0.728 > 0.726
Average MCC ± 95% Confidence Intervals 0.730 ± 0.030 > 0.718 ± 0.036
Sensitivity 0.697 > 0.614
Positive Predictive Value 0.760 < 0.860
Total TP 25763 > 22679
Total TN 104336584 < 104344087
Total FP 11045 > 5560
Total FP CONTRA 1367 > 629
Total FP INCONS 6752 > 3071
Total FP COMP 2926 > 1860
Total FN 11201 < 14285
P-value 6.06606238843e-08

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Performance plots


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

  3. Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(20) and CentroidAlifold(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 CentroidAlifold(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 CentroidAlifold(20) - scored lower 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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Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.