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Table of contents:

  1. Overview

  2. Performance Plots

  3. Performance of RNAalifold(20) - scored higher in this pairwise comparison

  4. Performance of RSpredict(20) - scored lower in this pairwise comparison

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


Overview

Metric RNAalifold(20) RSpredict(20)
MCC 0.674 > 0.464
Average MCC ± 95% Confidence Intervals 0.674 ± 0.044 > 0.472 ± 0.067
Sensitivity 0.621 > 0.417
Positive Predictive Value 0.732 > 0.516
Total TP 22941 > 15416
Total TN 104339145 < 104340583
Total FP 9959 < 16541
Total FP CONTRA 1517 < 2420
Total FP INCONS 6863 < 12047
Total FP COMP 1579 < 2074
Total FN 14023 < 21548
P-value 3.56938820447e-08

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Performance plots


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

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

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Performance of RNAalifold(20) - scored higher 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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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.