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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 MaxExpect - scored lower in this pairwise comparison

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


Overview

Metric RNAalifold(20) MaxExpect
MCC 0.674 > 0.415
Average MCC ± 95% Confidence Intervals 0.674 ± 0.044 > 0.416 ± 0.027
Sensitivity 0.621 > 0.406
Positive Predictive Value 0.732 > 0.424
Total TP 22941 > 15020
Total TN 104339145 > 104335019
Total FP 9959 < 22934
Total FP CONTRA 1517 < 3099
Total FP INCONS 6863 < 17328
Total FP COMP 1579 < 2507
Total FN 14023 < 21944
P-value 3.56938820447e-08

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Performance plots


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

  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 MaxExpect).

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

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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 MaxExpect - scored lower in this pairwise comparison

1. Total counts & total scores for MaxExpect

Total Base Pair Counts
Total TP 15020
Total TN 104335019
Total FP 22934
Total FP CONTRA 3099
Total FP INCONS 17328
Total FP COMP 2507
Total FN 21944
Total Scores
MCC 0.415
Average MCC ± 95% Confidence Intervals 0.416 ± 0.027
Sensitivity 0.406
Positive Predictive Value 0.424
Nr of predictions 77

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2. Individual counts for MaxExpect [ download as .csv ]

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.71 0.70 0.71 320 1085152 169 17 112 40 138
CRW_00034 0.66 0.65 0.66 310 1141844 191 28 134 29 164
CRW_00048 0.52 0.48 0.57 226 1170816 189 20 153 16 244
CRW_00054 0.43 0.42 0.44 192 1107377 261 23 224 14 264
CRW_00059 0.51 0.49 0.54 232 1172316 212 16 182 14 241
CRW_00061 0.44 0.43 0.45 203 1181497 266 35 218 13 273
CRW_00068 0.44 0.43 0.45 197 1108869 251 32 207 12 260
CRW_00096 0.49 0.47 0.52 220 1178453 229 21 186 22 245
CRW_00140 0.43 0.42 0.44 193 1135835 265 20 230 15 270
CRW_00141 0.54 0.53 0.55 254 1201566 230 30 175 25 222
CRW_00150 0.44 0.43 0.46 202 1152479 257 24 216 17 264
CRW_00152 0.58 0.55 0.60 259 1179986 190 37 134 19 212
CRW_00166 0.43 0.41 0.46 192 1190777 241 18 209 14 276
CRW_00173 0.26 0.26 0.27 115 1082230 324 28 283 13 330
CRW_00177 0.48 0.47 0.50 221 1178440 239 26 193 20 252
CRW_00196 0.50 0.49 0.51 233 1207782 238 32 188 18 242
CRW_00230 0.58 0.55 0.60 263 1198489 199 15 159 25 215
CRW_00245 0.42 0.41 0.43 186 1105895 262 25 222 15 267
CRW_00248 0.51 0.51 0.51 248 1218656 263 29 208 26 236
CRW_00250 0.51 0.50 0.51 241 1198458 244 44 183 17 237
CRW_00256 0.40 0.39 0.41 182 1192293 285 38 227 20 286
CRW_00270 0.54 0.54 0.55 244 1111842 223 23 177 23 211
CRW_00271 0.33 0.32 0.34 146 1122327 292 34 244 14 316
CRW_00273 0.42 0.40 0.45 180 1085197 237 27 197 13 266
CRW_00275 0.61 0.60 0.62 273 1114831 186 26 141 19 184
CRW_00277 0.35 0.33 0.37 148 1110390 267 37 220 10 305
CRW_00278 0.39 0.36 0.42 160 1129876 240 22 198 20 290
CRW_00279 0.54 0.53 0.56 244 1179977 213 26 169 18 220
CRW_00280 0.36 0.35 0.37 157 1117836 279 37 230 12 296
CRW_00281 0.59 0.58 0.60 270 1144891 201 25 155 21 194
CRW_00284 0.38 0.35 0.41 159 1131368 249 21 212 16 297
CRW_00285 0.56 0.54 0.58 246 1117835 199 26 153 20 212
CRW_00289 0.48 0.46 0.50 218 1189213 245 32 190 23 258
CRW_00298 0.24 0.25 0.24 123 1620380 438 79 318 41 371
CRW_00301 0.35 0.35 0.35 180 1761991 393 60 272 61 339
CRW_00306 0.18 0.19 0.18 86 1445370 462 62 332 68 376
CRW_00310 0.30 0.30 0.30 157 1805427 422 63 303 56 364
CRW_00326 0.41 0.41 0.42 205 1627618 330 55 232 43 297
CRW_00330 0.33 0.33 0.32 172 1988480 429 65 298 66 345
CRW_00332 0.18 0.18 0.17 87 1769512 473 87 335 51 390
CRW_00333 0.33 0.32 0.35 166 1892006 380 65 248 67 348
CRW_00345 0.35 0.35 0.36 174 1586388 361 52 257 52 324
CRW_00346 0.37 0.38 0.37 188 1584581 361 62 259 40 313
CRW_00348 0.31 0.30 0.33 151 1615043 353 51 258 44 352
CRW_00358 0.41 0.41 0.42 206 1674869 336 56 234 46 301
CRW_00366 0.27 0.28 0.26 134 1579236 421 78 305 38 348
CRW_00370 0.30 0.30 0.30 151 1640256 403 77 282 44 355
CRW_00371 0.40 0.39 0.42 192 1611452 316 45 221 50 304
CRW_00372 0.28 0.28 0.27 139 1625798 414 78 291 45 359
CRW_00379 0.44 0.44 0.43 234 2126414 384 57 248 79 300
CRW_00386 0.26 0.27 0.25 138 1750712 440 78 328 34 377
CRW_00403 0.31 0.31 0.31 144 1606062 415 58 264 93 320
CRW_00411 0.33 0.33 0.34 163 1615021 361 68 251 42 333
CRW_00414 0.30 0.31 0.30 153 1665712 421 60 300 61 342
CRW_00466 0.61 0.60 0.62 273 1116325 188 25 142 21 185
CRW_00589 0.32 0.31 0.34 136 1094057 285 28 239 18 309
CRW_00590 0.40 0.37 0.43 169 1119363 246 23 201 22 283
CRW_00591 0.44 0.43 0.44 194 1098463 264 36 210 18 252
CRW_00598 0.38 0.39 0.38 190 1665724 360 63 248 49 301
CRW_00758 0.33 0.32 0.34 155 1640308 356 41 262 53 328
CRW_00759 0.31 0.31 0.30 151 1636649 407 59 286 62 330
CRW_00760 0.29 0.29 0.28 143 1638449 415 65 298 52 343
CRW_00772 0.22 0.21 0.23 85 945632 297 29 254 14 319
CRW_00789 0.37 0.37 0.38 165 1137350 293 39 232 22 282
CRW_00795 0.35 0.35 0.35 138 1152523 307 34 226 47 256
CRW_00849 0.58 0.58 0.59 271 1117802 215 14 173 28 199
CRW_00997 0.44 0.42 0.45 197 1135837 260 32 212 16 267
CRW_01153 0.30 0.30 0.30 151 1606020 397 56 301 40 352
CRW_01171 0.33 0.33 0.34 167 1593511 375 57 270 48 339
CRW_01300 0.35 0.34 0.35 177 1693219 370 60 264 46 338
PDB_00703 0.57 0.52 0.62 259 1073427 187 20 139 28 236
PDB_00854 0.58 0.56 0.60 298 1500283 247 21 176 50 237
PDB_01088 0.33 0.32 0.35 176 1470965 353 46 283 24 371
PDB_01103 0.63 0.60 0.67 337 1606027 197 18 146 33 225
PDB_01105 0.57 0.54 0.60 289 1433488 229 24 170 35 251
PDB_01120 0.43 0.40 0.46 211 1204672 264 28 217 19 316
PDB_01273 0.45 0.43 0.46 211 1117804 273 31 214 28 280

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