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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 PETfold_pre2.0(20) - scored lower in this pairwise comparison

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


Overview

Metric PETfold_pre2.0(seed) PETfold_pre2.0(20)
MCC 0.760 > 0.728
Average MCC ± 95% Confidence Intervals 0.763 ± 0.022 > 0.730 ± 0.030
Sensitivity 0.730 > 0.697
Positive Predictive Value 0.792 > 0.760
Total TP 26994 > 25763
Total TN 104336380 < 104336584
Total FP 11076 > 11045
Total FP CONTRA 1094 < 1367
Total FP INCONS 5998 < 6752
Total FP COMP 3984 > 2926
Total FN 9970 < 11201
P-value 3.56938820447e-08

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Performance plots


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

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