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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 RNAalifold(20) - scored lower in this pairwise comparison

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


Overview

Metric CentroidAlifold(20) RNAalifold(20)
MCC 0.726 > 0.674
Average MCC ± 95% Confidence Intervals 0.718 ± 0.036 > 0.674 ± 0.044
Sensitivity 0.614 < 0.621
Positive Predictive Value 0.860 > 0.732
Total TP 22679 < 22941
Total TN 104344087 > 104339145
Total FP 5560 < 9959
Total FP CONTRA 629 < 1517
Total FP INCONS 3071 < 6863
Total FP COMP 1860 > 1579
Total FN 14285 > 14023
P-value 3.56938820447e-08

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Performance plots


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

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

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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 RNAalifold(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP 22941
Total TN 104339145
Total FP 9959
Total FP CONTRA 1517
Total FP INCONS 6863
Total FP COMP 1579
Total FN 14023
Total Scores
MCC 0.674
Average MCC ± 95% Confidence Intervals 0.674 ± 0.044
Sensitivity 0.621
Positive Predictive Value 0.732
Nr of predictions 77

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.87 0.84 0.90 385 1085172 61 7 37 17 73
CRW_00034 0.83 0.78 0.87 371 1141890 74 12 43 19 103
CRW_00048 0.83 0.80 0.86 374 1170779 75 11 51 13 96
CRW_00054 0.84 0.82 0.87 372 1107390 68 12 42 14 84
CRW_00059 0.81 0.76 0.86 361 1172324 71 11 50 10 112
CRW_00061 0.85 0.80 0.90 382 1181529 55 14 28 13 94
CRW_00068 0.86 0.83 0.89 381 1108875 61 12 37 12 76
CRW_00096 0.85 0.81 0.90 376 1178461 63 6 37 20 89
CRW_00140 0.84 0.82 0.87 380 1135841 71 13 44 14 83
CRW_00141 0.82 0.78 0.87 371 1201597 71 12 45 14 105
CRW_00150 0.84 0.80 0.88 372 1152500 62 12 37 13 94
CRW_00152 0.79 0.75 0.82 355 1179984 91 17 60 14 116
CRW_00166 0.83 0.79 0.88 368 1190777 71 7 44 20 100
CRW_00173 0.77 0.75 0.80 332 1082242 94 12 70 12 113
CRW_00177 0.80 0.76 0.84 358 1178455 78 13 54 11 115
CRW_00196 0.82 0.79 0.86 373 1207803 68 15 44 9 102
CRW_00230 0.83 0.79 0.88 378 1198495 67 12 41 14 100
CRW_00245 0.86 0.83 0.89 378 1105903 56 14 33 9 75
CRW_00248 0.79 0.75 0.83 364 1218705 87 17 55 15 120
CRW_00250 0.83 0.78 0.88 373 1198502 61 12 39 10 105
CRW_00256 0.82 0.78 0.87 363 1192322 68 14 41 13 105
CRW_00270 0.85 0.83 0.88 376 1111859 66 12 39 15 79
CRW_00271 0.82 0.79 0.87 363 1122332 69 11 45 13 99
CRW_00273 0.84 0.81 0.87 360 1085185 68 13 43 12 86
CRW_00275 0.84 0.81 0.87 368 1114849 68 12 42 14 89
CRW_00277 0.82 0.79 0.85 359 1110374 76 14 48 14 94
CRW_00278 0.82 0.78 0.86 349 1129851 72 10 46 16 101
CRW_00279 0.81 0.78 0.85 360 1179994 80 12 50 18 104
CRW_00280 0.83 0.79 0.87 360 1117845 71 12 43 16 93
CRW_00281 0.82 0.78 0.85 363 1144916 75 12 50 13 101
CRW_00284 0.84 0.80 0.89 363 1131350 62 12 35 15 93
CRW_00285 0.83 0.79 0.88 364 1117844 66 13 39 14 94
CRW_00289 0.81 0.76 0.86 361 1189232 70 13 47 10 115
CRW_00298 0.43 0.38 0.49 187 1620517 224 43 153 28 307
CRW_00301 0.42 0.37 0.48 192 1762101 229 37 173 19 327
CRW_00306 0.42 0.38 0.46 176 1445467 237 39 168 30 286
CRW_00310 0.46 0.39 0.55 204 1805579 190 29 138 23 317
CRW_00326 0.41 0.35 0.47 178 1627730 219 36 166 17 324
CRW_00330 0.40 0.35 0.47 182 1988624 243 35 174 34 335
CRW_00332 0.39 0.34 0.43 164 1769642 239 35 180 24 313
CRW_00333 0.34 0.29 0.40 150 1892114 241 34 187 20 364
CRW_00345 0.43 0.38 0.48 189 1586477 222 39 166 17 309
CRW_00346 0.45 0.40 0.50 202 1584688 230 32 168 30 299
CRW_00348 0.43 0.38 0.48 190 1615106 228 41 166 21 313
CRW_00358 0.43 0.38 0.49 192 1674972 227 34 167 26 315
CRW_00366 0.39 0.34 0.45 166 1579381 248 30 176 42 316
CRW_00370 0.52 0.47 0.57 240 1640342 204 34 150 20 266
CRW_00371 0.43 0.38 0.49 187 1611527 222 27 169 26 309
CRW_00372 0.40 0.35 0.46 174 1625925 228 37 170 21 324
CRW_00379 0.40 0.34 0.47 179 2126574 228 31 169 28 355
CRW_00386 0.44 0.37 0.51 193 1750879 199 35 149 15 322
CRW_00403 0.39 0.37 0.42 170 1606127 272 38 193 41 294
CRW_00411 0.43 0.39 0.48 191 1615105 227 43 164 20 305
CRW_00414 0.38 0.35 0.41 171 1665811 266 36 207 23 324
CRW_00466 0.84 0.81 0.86 373 1116333 74 11 48 15 85
CRW_00589 0.86 0.81 0.91 361 1094062 61 7 30 24 84
CRW_00590 0.84 0.79 0.89 358 1119354 70 6 38 26 94
CRW_00591 0.87 0.83 0.91 368 1098500 61 9 26 26 78
CRW_00598 0.42 0.38 0.47 187 1665825 229 39 174 16 304
CRW_00758 0.48 0.43 0.53 210 1640373 205 34 149 22 273
CRW_00759 0.42 0.38 0.48 182 1636762 232 39 162 31 299
CRW_00760 0.43 0.37 0.50 179 1638594 209 38 144 27 307
CRW_00772 0.78 0.74 0.83 298 945642 94 6 54 34 106
CRW_00789 0.82 0.78 0.87 348 1137388 80 6 44 30 99
CRW_00795 0.74 0.70 0.79 276 1152572 131 10 63 58 118
CRW_00849 0.78 0.74 0.82 350 1117832 97 13 65 19 120
CRW_00997 0.84 0.81 0.88 374 1135854 61 12 38 11 90
CRW_01153 0.47 0.42 0.53 210 1606133 216 27 158 31 293
CRW_01171 0.44 0.38 0.50 193 1593619 210 32 161 17 313
CRW_01300 0.52 0.45 0.59 231 1693331 174 31 127 16 284
PDB_00703 0.78 0.71 0.86 353 1073436 80 10 46 24 142
PDB_00854 0.75 0.65 0.86 347 1500373 97 7 51 39 188
PDB_01088 0.73 0.62 0.86 341 1471072 93 2 55 36 206
PDB_01103 0.75 0.65 0.87 364 1606111 77 8 45 24 198
PDB_01105 0.76 0.67 0.87 360 1433555 85 3 53 29 180
PDB_01120 0.72 0.65 0.80 341 1204702 101 13 72 16 186
PDB_01273 0.78 0.71 0.86 347 1117857 83 8 48 27 144

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