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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 RSpredict(20) - scored lower in this pairwise comparison

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


Overview

Metric PETfold_pre2.0(20) RSpredict(20)
MCC 0.728 > 0.464
Average MCC ± 95% Confidence Intervals 0.730 ± 0.030 > 0.472 ± 0.067
Sensitivity 0.697 > 0.417
Positive Predictive Value 0.760 > 0.516
Total TP 25763 > 15416
Total TN 104336584 < 104340583
Total FP 11045 < 16541
Total FP CONTRA 1367 < 2420
Total FP INCONS 6752 < 12047
Total FP COMP 2926 > 2074
Total FN 11201 < 21548
P-value 3.56938820447e-08

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Performance plots


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

  3. Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(20) and RSpredict(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 RSpredict(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 RSpredict(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP 15416
Total TN 104340583
Total FP 16541
Total FP CONTRA 2420
Total FP INCONS 12047
Total FP COMP 2074
Total FN 21548
Total Scores
MCC 0.464
Average MCC ± 95% Confidence Intervals 0.472 ± 0.067
Sensitivity 0.417
Positive Predictive Value 0.516
Nr of predictions 77

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.78 0.76 0.80 349 1085166 117 16 70 31 109
CRW_00034 0.60 0.50 0.71 239 1141980 119 16 81 22 235
CRW_00048 0.74 0.71 0.78 332 1170788 124 21 74 29 138
CRW_00054 0.72 0.68 0.76 308 1107412 121 17 79 25 148
CRW_00059 0.73 0.68 0.78 320 1172336 118 19 71 28 153
CRW_00061 0.63 0.55 0.72 260 1181590 123 18 85 20 216
CRW_00068 0.73 0.69 0.77 314 1108895 119 18 78 23 143
CRW_00096 0.73 0.69 0.78 320 1178470 123 16 74 33 145
CRW_00140 0.73 0.68 0.79 316 1135876 116 15 71 30 147
CRW_00141 0.72 0.67 0.77 320 1201607 124 19 79 26 156
CRW_00150 0.73 0.68 0.79 315 1152520 110 20 66 24 151
CRW_00152 0.71 0.65 0.77 308 1180015 120 17 76 27 163
CRW_00166 0.73 0.68 0.79 317 1190796 115 15 68 32 151
CRW_00173 0.68 0.63 0.74 281 1082274 126 20 81 25 164
CRW_00177 0.66 0.60 0.74 283 1178495 122 22 80 20 190
CRW_00196 0.71 0.67 0.76 316 1207819 125 23 77 25 159
CRW_00230 0.72 0.67 0.77 319 1198513 119 20 74 25 159
CRW_00245 0.70 0.63 0.78 285 1105963 105 14 66 25 168
CRW_00248 0.71 0.67 0.76 322 1218719 127 19 81 27 162
CRW_00250 0.72 0.66 0.78 317 1198517 119 19 73 27 161
CRW_00256 0.71 0.62 0.81 292 1192380 91 18 50 23 176
CRW_00270 0.68 0.60 0.77 272 1111934 101 13 67 21 183
CRW_00271 0.70 0.65 0.75 301 1122349 125 21 80 24 161
CRW_00273 0.67 0.60 0.76 266 1085250 106 16 69 21 180
CRW_00275 0.73 0.69 0.77 315 1114864 116 18 74 24 142
CRW_00277 0.62 0.54 0.71 244 1110451 120 17 83 20 209
CRW_00278 0.60 0.51 0.71 231 1129930 115 14 81 20 219
CRW_00279 0.71 0.66 0.75 308 1180005 131 20 83 28 156
CRW_00280 0.71 0.66 0.75 300 1117861 125 19 80 26 153
CRW_00281 0.72 0.67 0.77 311 1144937 123 15 78 30 153
CRW_00284 0.71 0.66 0.77 301 1131370 113 18 71 24 155
CRW_00285 0.64 0.55 0.73 254 1117913 115 15 78 22 204
CRW_00289 0.70 0.66 0.76 312 1189241 126 19 81 26 164
CRW_00298 0.01 0.01 0.01 3 1620508 410 63 326 21 491
CRW_00301 0.33 0.31 0.36 161 1762053 322 46 243 33 358
CRW_00306 0.37 0.34 0.39 158 1445446 293 34 212 47 304
CRW_00310 0.02 0.02 0.02 8 1805520 442 63 359 20 513
CRW_00326 0.36 0.34 0.38 172 1627656 314 50 232 32 330
CRW_00330 0.02 0.02 0.02 8 1988575 477 82 350 45 509
CRW_00332 0.01 0.01 0.01 3 1769654 389 59 305 25 474
CRW_00333 0.00 0.00 0.00 1 1892051 454 80 353 21 513
CRW_00345 0.02 0.02 0.02 8 1586488 384 57 318 9 490
CRW_00346 0.35 0.31 0.39 156 1584690 293 33 211 49 345
CRW_00348 0.00 0.00 0.00 0 1615104 410 69 330 11 503
CRW_00358 0.00 0.00 0.00 0 1674979 406 62 324 20 507
CRW_00366 0.01 0.01 0.01 4 1579393 371 66 290 15 478
CRW_00370 0.39 0.37 0.42 186 1640327 297 32 221 44 320
CRW_00371 0.02 0.02 0.02 8 1611495 424 63 344 17 488
CRW_00372 0.02 0.02 0.02 8 1625926 390 51 321 18 490
CRW_00379 0.00 0.00 0.00 0 2126541 465 66 346 53 534
CRW_00386 0.02 0.02 0.02 8 1750835 427 65 348 14 507
CRW_00403 0.00 0.00 0.00 0 1606168 385 68 292 25 464
CRW_00411 0.00 0.00 0.00 0 1615135 382 74 294 14 496
CRW_00414 0.33 0.31 0.36 152 1665808 305 45 220 40 343
CRW_00466 0.64 0.56 0.73 258 1116413 115 15 79 21 200
CRW_00589 0.64 0.55 0.75 244 1094136 105 9 71 25 201
CRW_00590 0.63 0.55 0.73 249 1119415 115 6 86 23 203
CRW_00591 0.70 0.63 0.76 283 1098533 118 13 74 31 163
CRW_00598 0.30 0.27 0.33 134 1665821 312 37 233 42 357
CRW_00758 0.00 0.00 0.00 0 1640340 444 79 347 18 483
CRW_00759 0.02 0.02 0.02 9 1636732 429 64 340 25 472
CRW_00760 0.00 0.00 0.00 0 1638553 425 77 325 23 486
CRW_00772 0.59 0.49 0.71 196 945723 109 10 71 28 208
CRW_00789 0.65 0.57 0.75 254 1137446 113 13 73 27 193
CRW_00795 0.63 0.53 0.75 209 1152644 114 10 58 46 185
CRW_00849 0.61 0.51 0.72 241 1117925 111 14 80 17 229
CRW_00997 0.73 0.69 0.77 319 1135862 125 18 79 28 145
CRW_01153 0.35 0.31 0.40 155 1606145 262 44 184 34 348
CRW_01171 0.02 0.01 0.02 7 1593610 403 61 327 15 499
CRW_01300 0.00 0.00 0.00 0 1693285 445 62 373 10 515
PDB_00703 0.67 0.60 0.75 297 1073447 132 13 88 31 198
PDB_00854 0.62 0.50 0.76 266 1500430 124 10 72 42 269
PDB_01088 0.62 0.49 0.77 268 1471123 123 8 71 44 279
PDB_01103 0.63 0.49 0.80 278 1606180 104 12 58 34 284
PDB_01105 0.61 0.50 0.75 270 1433609 124 8 84 32 270
PDB_01120 0.64 0.54 0.76 282 1204758 129 8 80 41 245
PDB_01273 0.69 0.62 0.77 305 1117865 121 14 76 31 186

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