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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 RSpredict(20) - scored lower in this pairwise comparison

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


Overview

Metric MXScarna(20) RSpredict(20)
MCC 0.598 > 0.464
Average MCC ± 95% Confidence Intervals 0.603 ± 0.029 > 0.472 ± 0.067
Sensitivity 0.548 > 0.417
Positive Predictive Value 0.653 > 0.516
Total TP 20251 > 15416
Total TN 104339447 < 104340583
Total FP 14477 < 16541
Total FP CONTRA 1798 < 2420
Total FP INCONS 8970 < 12047
Total FP COMP 3709 > 2074
Total FN 16713 < 21548
P-value 3.56938820447e-08

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Performance plots


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

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

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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 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.