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Table of contents:

  1. Overview

  2. Performance Plots

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

  4. Performance of UNAFold - scored lower in this pairwise comparison

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


Overview

Metric MXScarna(20) UNAFold
MCC 0.598 > 0.417
Average MCC ± 95% Confidence Intervals 0.603 ± 0.029 > 0.420 ± 0.033
Sensitivity 0.548 > 0.416
Positive Predictive Value 0.653 > 0.419
Total TP 20251 > 15359
Total TN 104339447 > 104333813
Total FP 14477 < 23719
Total FP CONTRA 1798 < 3462
Total FP INCONS 8970 < 17832
Total FP COMP 3709 > 2425
Total FN 16713 < 21605
P-value 3.56938820447e-08

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Performance plots


  1. Comparison of performance of MXScarna(20) and UNAFold. 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 MXScarna(20) and UNAFold).

  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 MXScarna(20) and UNAFold).

  3. Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(20) and UNAFold. 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 MXScarna(20) and UNAFold).

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Performance of MXScarna(20) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP 20251
Total TN 104339447
Total FP 14477
Total FP CONTRA 1798
Total FP INCONS 8970
Total FP COMP 3709
Total FN 16713
Total Scores
MCC 0.598
Average MCC ± 95% Confidence Intervals 0.603 ± 0.029
Sensitivity 0.548
Positive Predictive Value 0.653
Nr of predictions 77

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.84 0.81 0.87 369 1085176 107 10 46 51 89
CRW_00034 0.68 0.60 0.77 283 1141947 122 12 74 36 191
CRW_00048 0.72 0.67 0.78 317 1170807 127 11 80 36 153
CRW_00054 0.68 0.63 0.74 288 1107425 137 16 87 34 168
CRW_00059 0.72 0.66 0.78 312 1172344 127 16 74 37 161
CRW_00061 0.73 0.66 0.81 316 1181563 109 13 61 35 160
CRW_00068 0.69 0.64 0.74 293 1108909 137 18 85 34 164
CRW_00096 0.75 0.68 0.81 318 1178489 108 6 67 35 147
CRW_00140 0.76 0.71 0.81 328 1135874 114 12 64 38 135
CRW_00141 0.69 0.64 0.75 305 1201619 132 14 87 31 171
CRW_00150 0.72 0.65 0.80 303 1152540 113 14 64 35 163
CRW_00152 0.76 0.70 0.82 332 1180009 110 11 64 35 139
CRW_00166 0.65 0.60 0.71 281 1190800 160 10 105 45 187
CRW_00173 0.57 0.52 0.63 232 1082285 168 19 120 29 213
CRW_00177 0.62 0.56 0.68 264 1178492 152 16 108 28 209
CRW_00196 0.73 0.67 0.80 319 1207837 117 10 69 38 156
CRW_00230 0.73 0.67 0.80 319 1198526 122 12 69 41 159
CRW_00245 0.73 0.67 0.81 302 1105955 106 13 58 35 151
CRW_00248 0.71 0.65 0.77 317 1218729 129 13 82 34 167
CRW_00250 0.73 0.67 0.79 321 1198521 119 12 72 35 157
CRW_00256 0.70 0.64 0.77 299 1192353 124 11 77 36 169
CRW_00270 0.72 0.67 0.77 306 1111891 121 14 75 32 149
CRW_00271 0.70 0.65 0.77 298 1122364 122 17 72 33 164
CRW_00273 0.68 0.62 0.74 277 1085225 135 13 86 36 169
CRW_00275 0.71 0.63 0.80 289 1114908 114 13 61 40 168
CRW_00277 0.68 0.63 0.73 286 1110405 132 17 87 28 167
CRW_00278 0.71 0.62 0.80 280 1129906 107 12 58 37 170
CRW_00279 0.70 0.64 0.77 299 1180027 133 10 80 43 165
CRW_00280 0.72 0.66 0.78 301 1117875 125 10 74 41 152
CRW_00281 0.71 0.65 0.78 303 1144954 117 13 71 33 161
CRW_00284 0.69 0.62 0.77 281 1131397 117 9 73 35 175
CRW_00285 0.70 0.64 0.77 292 1117883 123 15 70 38 166
CRW_00289 0.62 0.58 0.66 274 1189239 172 18 122 32 202
CRW_00298 0.48 0.46 0.51 226 1620454 284 45 175 64 268
CRW_00301 0.42 0.39 0.45 204 1762046 308 49 204 55 315
CRW_00306 0.43 0.40 0.46 183 1445453 276 47 167 62 279
CRW_00310 0.45 0.41 0.49 212 1805516 285 39 183 63 309
CRW_00326 0.49 0.45 0.53 227 1627679 267 35 169 63 275
CRW_00330 0.41 0.37 0.45 190 1988597 294 32 196 66 327
CRW_00332 0.37 0.34 0.40 163 1769615 307 47 196 64 314
CRW_00333 0.31 0.26 0.35 136 1892099 328 47 203 78 378
CRW_00345 0.46 0.44 0.49 219 1586422 293 53 177 63 279
CRW_00346 0.49 0.46 0.52 229 1584649 269 43 169 57 272
CRW_00348 0.49 0.47 0.52 235 1615052 277 51 165 61 268
CRW_00358 0.48 0.44 0.53 224 1674941 262 38 162 62 283
CRW_00366 0.42 0.40 0.43 195 1579299 332 47 212 73 287
CRW_00370 0.50 0.48 0.52 242 1640302 281 47 175 59 264
CRW_00371 0.49 0.46 0.53 229 1611474 266 39 168 59 267
CRW_00372 0.51 0.47 0.54 236 1625872 273 37 161 75 262
CRW_00379 0.37 0.33 0.42 175 2126532 323 40 206 77 359
CRW_00386 0.47 0.43 0.50 223 1750812 281 44 177 60 292
CRW_00403 0.45 0.41 0.48 192 1606131 304 37 168 99 272
CRW_00411 0.49 0.46 0.52 227 1615066 271 42 168 61 269
CRW_00414 0.39 0.37 0.41 181 1665782 316 50 212 54 314
CRW_00466 0.63 0.58 0.69 266 1116382 147 16 101 30 192
CRW_00589 0.69 0.62 0.76 277 1094097 130 6 80 44 168
CRW_00590 0.72 0.67 0.78 303 1119366 134 11 76 47 149
CRW_00591 0.74 0.68 0.81 303 1098531 115 7 62 46 143
CRW_00598 0.49 0.46 0.52 226 1665793 276 41 165 70 265
CRW_00758 0.46 0.43 0.48 207 1640338 292 44 177 71 276
CRW_00759 0.42 0.40 0.44 191 1636712 314 43 199 72 290
CRW_00760 0.46 0.43 0.49 208 1638533 291 37 177 77 278
CRW_00772 0.60 0.54 0.67 217 945677 148 10 96 42 187
CRW_00789 0.67 0.60 0.75 268 1137427 134 8 83 43 179
CRW_00795 0.63 0.57 0.71 224 1152605 176 10 82 84 170
CRW_00849 0.61 0.55 0.68 260 1117878 154 17 105 32 210
CRW_00997 0.74 0.69 0.79 322 1135872 121 12 72 37 142
CRW_01153 0.44 0.42 0.46 211 1606072 295 46 199 50 292
CRW_01171 0.48 0.45 0.51 229 1593556 274 47 173 54 277
CRW_01300 0.47 0.45 0.50 230 1693258 286 45 187 54 285
PDB_00703 0.69 0.60 0.79 295 1073472 114 10 68 36 200
PDB_00854 0.62 0.51 0.75 274 1500415 142 2 87 53 261
PDB_01088 0.66 0.56 0.78 308 1471077 135 7 78 50 239
PDB_01103 0.61 0.52 0.71 293 1606118 156 16 101 39 269
PDB_01105 0.64 0.54 0.75 291 1433583 134 3 94 37 249
PDB_01120 0.66 0.57 0.76 302 1204732 134 11 83 40 225
PDB_01273 0.69 0.60 0.79 294 1117886 120 10 70 40 197

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Performance of UNAFold - scored lower in this pairwise comparison

1. Total counts & total scores for UNAFold

Total Base Pair Counts
Total TP 15359
Total TN 104333813
Total FP 23719
Total FP CONTRA 3462
Total FP INCONS 17832
Total FP COMP 2425
Total FN 21605
Total Scores
MCC 0.417
Average MCC ± 95% Confidence Intervals 0.420 ± 0.033
Sensitivity 0.416
Positive Predictive Value 0.419
Nr of predictions 77

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.77 0.76 0.78 347 1085158 132 19 77 36 111
CRW_00034 0.64 0.64 0.64 303 1141840 196 31 142 23 171
CRW_00048 0.52 0.51 0.53 241 1170762 229 24 188 17 229
CRW_00054 0.44 0.43 0.44 195 1107376 258 28 217 13 261
CRW_00059 0.49 0.48 0.50 227 1172295 238 32 192 14 246
CRW_00061 0.51 0.51 0.52 241 1181493 233 41 178 14 235
CRW_00068 0.46 0.46 0.47 209 1108862 250 23 211 16 248
CRW_00096 0.55 0.54 0.55 250 1178428 227 29 173 25 215
CRW_00140 0.66 0.65 0.67 303 1135826 172 19 130 23 160
CRW_00141 0.58 0.58 0.59 275 1201557 219 25 168 26 201
CRW_00150 0.41 0.41 0.42 190 1152471 280 32 228 20 276
CRW_00152 0.65 0.63 0.66 299 1179965 174 29 123 22 172
CRW_00166 0.45 0.44 0.45 207 1190736 269 34 219 16 261
CRW_00173 0.28 0.28 0.29 126 1082215 327 39 276 12 319
CRW_00177 0.51 0.49 0.53 234 1178440 221 29 177 15 239
CRW_00196 0.45 0.44 0.45 211 1207765 281 32 227 22 264
CRW_00230 0.55 0.54 0.57 256 1198474 218 27 169 22 222
CRW_00245 0.36 0.36 0.37 163 1105885 293 45 235 13 290
CRW_00248 0.58 0.57 0.58 276 1218667 230 24 174 32 208
CRW_00250 0.39 0.39 0.39 186 1198451 301 43 246 12 292
CRW_00256 0.50 0.49 0.52 228 1192304 228 35 173 20 240
CRW_00270 0.47 0.45 0.48 207 1111853 250 29 197 24 248
CRW_00271 0.48 0.47 0.50 217 1122314 236 33 187 16 245
CRW_00273 0.51 0.50 0.52 222 1085175 222 28 176 18 224
CRW_00275 0.68 0.68 0.69 310 1114822 160 19 120 21 147
CRW_00277 0.35 0.34 0.35 154 1110361 293 42 238 13 299
CRW_00278 0.43 0.41 0.44 186 1129832 259 29 209 21 264
CRW_00279 0.44 0.42 0.45 197 1179977 258 31 211 16 267
CRW_00280 0.68 0.67 0.68 302 1117819 159 19 120 20 151
CRW_00281 0.65 0.63 0.67 291 1144909 165 18 123 24 173
CRW_00284 0.29 0.28 0.29 129 1131319 325 39 273 13 327
CRW_00285 0.75 0.74 0.76 338 1117818 130 22 82 26 120
CRW_00289 0.44 0.43 0.45 203 1189200 274 30 220 24 273
CRW_00298 0.22 0.23 0.22 114 1620379 443 82 325 36 380
CRW_00301 0.31 0.31 0.30 163 1761959 431 87 294 50 356
CRW_00306 0.16 0.16 0.16 76 1445368 444 67 339 38 386
CRW_00310 0.26 0.27 0.26 141 1805406 466 81 322 63 380
CRW_00326 0.35 0.35 0.35 176 1627600 377 65 269 43 326
CRW_00330 0.29 0.31 0.28 158 1988457 459 73 327 59 359
CRW_00332 0.21 0.22 0.20 104 1769488 470 103 326 41 373
CRW_00333 0.33 0.33 0.32 169 1891961 426 77 278 71 345
CRW_00345 0.27 0.28 0.27 138 1586355 422 75 303 44 360
CRW_00346 0.30 0.31 0.29 155 1584555 401 76 304 21 346
CRW_00348 0.26 0.26 0.26 131 1615002 412 57 313 42 372
CRW_00358 0.39 0.39 0.39 200 1674848 370 67 250 53 307
CRW_00366 0.33 0.35 0.32 167 1579237 391 83 266 42 315
CRW_00370 0.25 0.26 0.25 130 1640246 437 74 316 47 376
CRW_00371 0.31 0.32 0.30 159 1611384 399 75 292 32 337
CRW_00372 0.36 0.36 0.36 180 1625800 366 59 267 40 318
CRW_00379 0.40 0.40 0.39 215 2126404 429 56 278 95 319
CRW_00386 0.25 0.27 0.24 137 1750675 476 78 366 32 378
CRW_00403 0.31 0.31 0.30 146 1606048 418 64 270 84 318
CRW_00411 0.27 0.28 0.27 138 1614990 413 60 315 38 358
CRW_00414 0.30 0.31 0.29 154 1665688 426 77 306 43 341
CRW_00466 0.59 0.58 0.61 265 1116332 195 23 145 27 193
CRW_00589 0.28 0.27 0.29 121 1094037 315 38 264 13 324
CRW_00590 0.35 0.34 0.37 153 1119337 287 30 236 21 299
CRW_00591 0.56 0.54 0.58 243 1098483 208 22 155 31 203
CRW_00598 0.36 0.37 0.35 183 1665703 391 62 277 52 308
CRW_00758 0.28 0.29 0.27 138 1640264 418 60 304 54 345
CRW_00759 0.23 0.24 0.22 117 1636617 466 66 345 55 364
CRW_00760 0.31 0.31 0.32 151 1638482 393 57 265 71 335
CRW_00772 0.25 0.25 0.26 101 945612 317 39 248 30 303
CRW_00789 0.34 0.33 0.34 147 1137356 300 35 248 17 300
CRW_00795 0.19 0.20 0.19 78 1152508 377 53 282 42 316
CRW_00849 0.48 0.48 0.49 225 1117800 258 25 210 23 245
CRW_00997 0.59 0.58 0.61 268 1135838 197 24 148 25 196
CRW_01153 0.25 0.25 0.25 128 1606016 421 65 319 37 375
CRW_01171 0.24 0.24 0.24 123 1593484 433 84 314 35 383
CRW_01300 0.37 0.37 0.36 193 1693178 383 91 258 34 322
PDB_00703 0.54 0.52 0.57 258 1073389 221 20 178 23 237
PDB_00854 0.54 0.53 0.54 285 1500255 284 22 216 46 250
PDB_01088 0.39 0.37 0.41 202 1470973 322 44 251 27 345
PDB_01103 0.59 0.58 0.60 324 1605991 243 32 181 30 238
PDB_01105 0.60 0.58 0.61 315 1433457 227 14 185 28 225
PDB_01120 0.47 0.44 0.50 232 1204667 242 27 202 13 295
PDB_01273 0.50 0.48 0.53 235 1117815 238 14 196 28 256

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