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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 RSpredict(20) - scored lower in this pairwise comparison

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


Overview

Metric PETfold_pre2.0(seed) RSpredict(20)
MCC 0.760 > 0.464
Average MCC ± 95% Confidence Intervals 0.763 ± 0.022 > 0.472 ± 0.067
Sensitivity 0.730 > 0.417
Positive Predictive Value 0.792 > 0.516
Total TP 26994 > 15416
Total TN 104336380 < 104340583
Total FP 11076 < 16541
Total FP CONTRA 1094 < 2420
Total FP INCONS 5998 < 12047
Total FP COMP 3984 > 2074
Total FN 9970 < 21548
P-value 3.56938820447e-08

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Performance plots


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

  3. Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) 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(seed) and RSpredict(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 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.