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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric CentroidAlifold(20) RSpredict(20)
MCC 0.726 > 0.464
Average MCC ± 95% Confidence Intervals 0.718 ± 0.036 > 0.472 ± 0.067
Sensitivity 0.614 > 0.417
Positive Predictive Value 0.860 > 0.516
Total TP 22679 > 15416
Total TN 104344087 > 104340583
Total FP 5560 < 16541
Total FP CONTRA 629 < 2420
Total FP INCONS 3071 < 12047
Total FP COMP 1860 < 2074
Total FN 14285 < 21548
P-value 3.56938820447e-08

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Performance plots


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

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

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

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

Total Base Pair Counts
Total TP 22679
Total TN 104344087
Total FP 5560
Total FP CONTRA 629
Total FP INCONS 3071
Total FP COMP 1860
Total FN 14285
Total Scores
MCC 0.726
Average MCC ± 95% Confidence Intervals 0.718 ± 0.036
Sensitivity 0.614
Positive Predictive Value 0.860
Nr of predictions 77

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.91 0.86 0.95 394 1085188 51 6 13 32 64
CRW_00034 0.83 0.77 0.90 365 1141911 54 9 31 14 109
CRW_00048 0.86 0.80 0.93 374 1170812 45 10 19 16 96
CRW_00054 0.86 0.80 0.93 364 1107423 43 10 19 14 92
CRW_00059 0.85 0.78 0.93 368 1172351 42 9 18 15 105
CRW_00061 0.86 0.80 0.92 380 1181542 47 10 21 16 96
CRW_00068 0.85 0.80 0.91 365 1108906 48 11 23 14 92
CRW_00096 0.86 0.78 0.95 363 1178497 43 4 16 23 102
CRW_00140 0.86 0.80 0.92 372 1135875 46 11 20 15 91
CRW_00141 0.85 0.78 0.93 371 1201625 47 10 19 18 105
CRW_00150 0.86 0.80 0.92 372 1152515 48 10 24 14 94
CRW_00152 0.84 0.77 0.91 364 1180015 52 13 24 15 107
CRW_00166 0.86 0.78 0.94 364 1190809 45 4 19 22 104
CRW_00173 0.80 0.75 0.86 332 1082272 67 11 41 15 113
CRW_00177 0.83 0.75 0.92 356 1178493 48 7 24 17 117
CRW_00196 0.86 0.79 0.94 377 1207832 45 8 18 19 98
CRW_00230 0.86 0.79 0.94 378 1198524 39 8 16 15 100
CRW_00245 0.87 0.81 0.93 367 1105932 46 9 20 17 86
CRW_00248 0.85 0.77 0.92 375 1218735 46 11 20 15 109
CRW_00250 0.84 0.77 0.92 370 1198524 46 11 21 14 108
CRW_00256 0.84 0.77 0.91 360 1192345 51 10 25 16 108
CRW_00270 0.86 0.80 0.92 362 1111893 46 11 20 15 93
CRW_00271 0.84 0.77 0.91 355 1122363 48 8 25 15 107
CRW_00273 0.86 0.79 0.92 354 1085218 46 8 21 17 92
CRW_00275 0.87 0.81 0.93 371 1114870 46 9 21 16 86
CRW_00277 0.85 0.78 0.91 354 1110408 50 12 21 17 99
CRW_00278 0.84 0.78 0.91 351 1129869 54 7 29 18 99
CRW_00279 0.84 0.77 0.92 357 1180030 50 8 21 21 107
CRW_00280 0.84 0.79 0.89 357 1117860 63 9 34 20 96
CRW_00281 0.84 0.77 0.92 357 1144951 49 9 24 16 107
CRW_00284 0.84 0.77 0.91 350 1131377 50 7 26 17 106
CRW_00285 0.83 0.77 0.90 353 1117869 56 11 27 18 105
CRW_00289 0.82 0.75 0.91 356 1189260 53 9 28 16 120
CRW_00298 0.52 0.37 0.72 183 1620647 90 6 64 20 311
CRW_00301 0.47 0.34 0.64 178 1762223 133 11 91 31 341
CRW_00306 0.52 0.37 0.73 171 1445616 97 6 57 34 291
CRW_00310 0.49 0.37 0.66 192 1805657 126 13 88 25 329
CRW_00326 0.57 0.40 0.80 201 1627859 78 6 44 28 301
CRW_00330 0.51 0.37 0.71 190 1988747 113 10 68 35 327
CRW_00332 0.48 0.34 0.67 161 1769781 123 8 71 44 316
CRW_00333 0.43 0.30 0.61 155 1892229 131 20 81 30 359
CRW_00345 0.51 0.36 0.72 181 1586621 96 8 61 27 317
CRW_00346 0.53 0.38 0.74 192 1584829 102 6 63 33 309
CRW_00348 0.54 0.40 0.72 200 1615226 107 10 67 30 303
CRW_00358 0.53 0.39 0.73 196 1675098 99 8 63 28 311
CRW_00366 0.52 0.37 0.71 180 1579501 100 8 64 28 302
CRW_00370 0.58 0.41 0.83 208 1640515 64 4 39 21 298
CRW_00371 0.55 0.40 0.75 199 1611646 93 8 57 28 297
CRW_00372 0.50 0.37 0.69 182 1626042 112 11 71 30 316
CRW_00379 0.49 0.33 0.72 176 2126710 109 5 62 42 358
CRW_00386 0.51 0.35 0.73 182 1751006 96 7 61 28 333
CRW_00403 0.52 0.39 0.70 180 1606270 126 11 67 48 284
CRW_00411 0.51 0.38 0.68 189 1615224 117 8 82 27 307
CRW_00414 0.48 0.34 0.67 170 1665972 109 11 72 26 325
CRW_00466 0.86 0.79 0.93 364 1116372 45 9 20 16 94
CRW_00589 0.86 0.78 0.94 347 1094091 45 2 20 23 98
CRW_00590 0.86 0.79 0.93 359 1119369 53 3 25 25 93
CRW_00591 0.86 0.79 0.92 354 1098520 55 6 23 26 92
CRW_00598 0.49 0.34 0.70 169 1665982 103 5 69 29 322
CRW_00758 0.52 0.38 0.72 184 1640510 108 6 66 36 299
CRW_00759 0.51 0.38 0.69 181 1636884 113 8 72 33 300
CRW_00760 0.52 0.37 0.74 180 1638713 102 7 55 40 306
CRW_00772 0.79 0.73 0.85 295 945652 81 5 48 28 109
CRW_00789 0.83 0.76 0.91 340 1137411 63 5 30 28 107
CRW_00795 0.80 0.72 0.88 284 1152598 97 3 36 58 110
CRW_00849 0.82 0.76 0.88 357 1117854 65 10 39 16 113
CRW_00997 0.85 0.80 0.91 369 1135873 50 13 23 14 95
CRW_01153 0.50 0.36 0.69 179 1606270 108 8 71 29 324
CRW_01171 0.49 0.36 0.67 183 1593733 116 11 78 27 323
CRW_01300 0.55 0.40 0.76 205 1693451 88 6 58 24 310
PDB_00703 0.81 0.70 0.92 348 1073468 55 8 21 26 147
PDB_00854 0.77 0.65 0.90 348 1500393 73 4 33 36 187
PDB_01088 0.75 0.62 0.90 341 1471090 76 2 37 37 206
PDB_01103 0.77 0.64 0.92 361 1606134 59 8 25 26 201
PDB_01105 0.78 0.66 0.92 359 1433581 59 2 29 28 181
PDB_01120 0.79 0.68 0.92 357 1204739 53 7 25 21 170
PDB_01273 0.80 0.69 0.91 341 1117886 62 6 27 29 150

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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.