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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric RSpredict(20) Sfold
MCC 0.464 > 0.453
Average MCC ± 95% Confidence Intervals 0.472 ± 0.067 > 0.455 ± 0.031
Sensitivity 0.417 > 0.403
Positive Predictive Value 0.516 > 0.510
Total TP 15416 > 14880
Total TN 104340583 < 104341300
Total FP 16541 > 16483
Total FP CONTRA 2420 > 2320
Total FP INCONS 12047 > 11966
Total FP COMP 2074 < 2197
Total FN 21548 < 22084
P-value 1.02208072244e-07

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Performance plots


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

  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 RSpredict(20) and Sfold).

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

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Performance of RSpredict(20) - scored higher 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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Performance of Sfold - scored lower in this pairwise comparison

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP 14880
Total TN 104341300
Total FP 16483
Total FP CONTRA 2320
Total FP INCONS 11966
Total FP COMP 2197
Total FN 22084
Total Scores
MCC 0.453
Average MCC ± 95% Confidence Intervals 0.455 ± 0.031
Sensitivity 0.403
Positive Predictive Value 0.510
Nr of predictions 77

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.80 0.77 0.83 352 1085176 112 13 60 39 106
CRW_00034 0.65 0.64 0.66 304 1141856 180 27 129 24 170
CRW_00048 0.50 0.45 0.54 213 1170824 198 17 161 20 257
CRW_00054 0.48 0.43 0.54 195 1107453 185 23 145 17 261
CRW_00059 0.54 0.49 0.60 232 1172361 169 19 134 16 241
CRW_00061 0.49 0.45 0.54 215 1181555 193 31 152 10 261
CRW_00068 0.48 0.43 0.53 196 1108938 184 19 152 13 261
CRW_00096 0.59 0.55 0.63 258 1178469 180 16 137 27 207
CRW_00140 0.66 0.60 0.73 280 1135893 125 10 95 20 183
CRW_00141 0.63 0.57 0.70 272 1201636 139 16 101 22 204
CRW_00150 0.40 0.37 0.44 171 1152531 233 30 189 14 295
CRW_00152 0.67 0.61 0.74 287 1180029 118 21 79 18 184
CRW_00166 0.54 0.47 0.61 221 1190832 160 15 128 17 247
CRW_00173 0.36 0.32 0.39 144 1082291 233 16 205 12 301
CRW_00177 0.45 0.41 0.50 195 1178491 206 27 167 12 278
CRW_00196 0.47 0.44 0.50 210 1207811 232 23 191 18 265
CRW_00230 0.61 0.53 0.70 254 1198565 129 7 100 22 224
CRW_00245 0.54 0.45 0.66 202 1106023 115 16 87 12 251
CRW_00248 0.58 0.57 0.59 274 1218677 223 21 169 33 210
CRW_00250 0.50 0.46 0.54 221 1198516 206 28 161 17 257
CRW_00256 0.37 0.33 0.42 155 1192370 232 35 180 17 313
CRW_00270 0.48 0.39 0.59 178 1111985 137 19 104 14 277
CRW_00271 0.49 0.43 0.57 198 1122402 170 32 119 19 264
CRW_00273 0.55 0.50 0.61 224 1085232 162 22 123 17 222
CRW_00275 0.58 0.47 0.73 213 1114978 98 14 66 18 244
CRW_00277 0.40 0.30 0.54 136 1110544 127 18 97 12 317
CRW_00278 0.51 0.37 0.70 166 1130018 88 6 66 16 284
CRW_00279 0.61 0.54 0.69 252 1180052 131 20 92 19 212
CRW_00280 0.60 0.55 0.66 250 1117881 149 21 108 20 203
CRW_00281 0.68 0.60 0.77 279 1144977 109 11 74 24 185
CRW_00284 0.42 0.33 0.53 149 1131480 147 20 111 16 307
CRW_00285 0.77 0.71 0.83 326 1117866 94 16 52 26 132
CRW_00289 0.59 0.51 0.68 241 1189298 141 19 95 27 235
CRW_00298 0.19 0.17 0.21 84 1620496 355 58 262 35 410
CRW_00301 0.33 0.30 0.36 156 1762064 326 45 238 43 363
CRW_00306 0.21 0.19 0.24 88 1445476 332 57 229 46 374
CRW_00310 0.30 0.26 0.35 138 1805554 298 56 202 40 383
CRW_00326 0.46 0.37 0.56 187 1627778 175 32 113 30 315
CRW_00330 0.34 0.28 0.41 145 1988661 279 50 159 70 372
CRW_00332 0.22 0.21 0.24 102 1769589 370 75 255 40 375
CRW_00333 0.30 0.30 0.31 153 1891989 400 68 275 57 361
CRW_00345 0.40 0.35 0.45 173 1586487 244 36 175 33 325
CRW_00346 0.34 0.32 0.36 161 1584648 319 58 223 38 340
CRW_00348 0.32 0.26 0.40 129 1615184 223 34 156 33 374
CRW_00358 0.38 0.33 0.43 166 1674980 241 44 175 22 341
CRW_00366 0.36 0.35 0.36 169 1579286 334 74 224 36 313
CRW_00370 0.34 0.32 0.36 160 1640327 325 54 225 46 346
CRW_00371 0.38 0.34 0.42 171 1611504 271 50 185 36 325
CRW_00372 0.39 0.35 0.45 172 1625925 245 34 175 36 326
CRW_00379 0.44 0.34 0.58 183 2126636 205 17 117 71 351
CRW_00386 0.29 0.27 0.31 138 1750806 345 60 252 33 377
CRW_00403 0.31 0.30 0.32 137 1606104 362 58 229 75 327
CRW_00411 0.39 0.32 0.47 157 1615171 217 28 147 42 339
CRW_00414 0.33 0.29 0.38 146 1665840 278 40 199 39 349
CRW_00466 0.57 0.54 0.61 247 1116358 185 18 142 25 211
CRW_00589 0.31 0.26 0.36 116 1094139 220 19 186 15 329
CRW_00590 0.58 0.40 0.84 179 1119542 50 5 30 15 273
CRW_00591 0.60 0.56 0.65 248 1098523 153 22 110 21 198
CRW_00598 0.35 0.34 0.37 165 1665773 333 62 225 46 326
CRW_00758 0.34 0.30 0.38 147 1640380 287 42 197 48 336
CRW_00759 0.23 0.22 0.25 105 1636722 354 42 276 36 376
CRW_00760 0.33 0.27 0.39 133 1638613 257 32 177 48 353
CRW_00772 0.30 0.27 0.34 108 945681 233 27 184 22 296
CRW_00789 0.40 0.34 0.46 152 1137458 193 30 146 17 295
CRW_00795 0.19 0.17 0.20 68 1152586 311 44 223 44 326
CRW_00849 0.50 0.48 0.52 227 1117826 230 18 189 23 243
CRW_00997 0.59 0.52 0.66 241 1135913 144 19 105 20 223
CRW_01153 0.37 0.30 0.45 152 1606193 221 35 148 38 351
CRW_01171 0.33 0.29 0.38 149 1593608 285 55 193 37 357
CRW_01300 0.39 0.34 0.45 175 1693327 254 42 176 36 340
PDB_00703 0.52 0.46 0.58 229 1073451 189 12 153 24 266
PDB_00854 0.54 0.49 0.60 263 1500337 220 22 156 42 272
PDB_01088 0.38 0.32 0.47 173 1471098 222 33 166 23 374
PDB_01103 0.56 0.50 0.63 280 1606082 191 20 146 25 282
PDB_01105 0.60 0.53 0.67 288 1433540 169 14 129 26 252
PDB_01120 0.55 0.44 0.70 230 1204799 110 12 87 11 297
PDB_01273 0.50 0.46 0.54 227 1117836 223 19 178 26 264

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