CompaRNA - on-line benchmarks of RNA structure prediction methods
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Table of contents:

  1. Overview

  2. Performance Plots

  3. Performance of PETfold_pre2.0(20) - scored higher in this pairwise comparison

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

  5. Compile and download dataset for PETfold_pre2.0(20) & Carnac(20) [.zip] - may take several seconds...


Overview

Metric PETfold_pre2.0(20) Carnac(20)
MCC 0.728 > 0.558
Average MCC ± 95% Confidence Intervals 0.730 ± 0.030 > 0.553 ± 0.023
Sensitivity 0.697 > 0.348
Positive Predictive Value 0.760 < 0.895
Total TP 25763 > 12872
Total TN 104336584 < 104356083
Total FP 11045 > 2613
Total FP CONTRA 1367 > 170
Total FP INCONS 6752 > 1341
Total FP COMP 2926 > 1102
Total FN 11201 < 24092
P-value 3.56938820447e-08

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Performance plots


  1. Comparison of performance of PETfold_pre2.0(20) and Carnac(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 PETfold_pre2.0(20) and Carnac(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 PETfold_pre2.0(20) and Carnac(20)).

  3. Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(20) and Carnac(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 PETfold_pre2.0(20) and Carnac(20)).

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Performance of PETfold_pre2.0(20) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(20)

Total Base Pair Counts
Total TP 25763
Total TN 104336584
Total FP 11045
Total FP CONTRA 1367
Total FP INCONS 6752
Total FP COMP 2926
Total FN 11201
Total Scores
MCC 0.728
Average MCC ± 95% Confidence Intervals 0.730 ± 0.030
Sensitivity 0.697
Positive Predictive Value 0.760
Nr of predictions 77

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2. Individual counts for PETfold_pre2.0(20) [ download as .csv ]

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.89 0.88 0.90 404 1085151 82 10 36 36 54
CRW_00034 0.82 0.79 0.85 374 1141875 86 17 50 19 100
CRW_00048 0.84 0.83 0.84 390 1170753 91 18 54 19 80
CRW_00054 0.84 0.84 0.84 381 1107361 95 17 57 21 75
CRW_00059 0.84 0.82 0.85 390 1172289 85 17 50 18 83
CRW_00061 0.84 0.82 0.86 390 1181501 85 16 46 23 86
CRW_00068 0.84 0.84 0.84 383 1108851 87 16 55 16 74
CRW_00096 0.85 0.83 0.87 388 1178436 81 12 44 25 77
CRW_00140 0.85 0.84 0.86 388 1135827 85 15 48 22 75
CRW_00141 0.83 0.81 0.85 387 1201568 90 18 52 20 89
CRW_00150 0.83 0.82 0.85 381 1152473 90 16 51 23 85
CRW_00152 0.83 0.81 0.85 381 1179968 89 17 50 22 90
CRW_00166 0.85 0.83 0.86 387 1190748 90 11 50 29 81
CRW_00173 0.80 0.80 0.81 354 1082220 107 18 64 25 91
CRW_00177 0.82 0.81 0.84 382 1178424 101 17 57 27 91
CRW_00196 0.83 0.81 0.85 387 1207780 91 16 52 23 88
CRW_00230 0.85 0.82 0.87 394 1198472 81 16 44 21 84
CRW_00245 0.87 0.86 0.87 390 1105881 79 17 40 22 63
CRW_00248 0.84 0.82 0.87 396 1218684 87 15 46 26 88
CRW_00250 0.83 0.80 0.85 382 1198478 88 15 51 22 96
CRW_00256 0.83 0.81 0.85 379 1192296 87 16 49 22 89
CRW_00270 0.86 0.86 0.86 390 1111833 85 15 48 22 65
CRW_00271 0.82 0.81 0.84 375 1122302 98 14 60 24 87
CRW_00273 0.84 0.84 0.84 375 1085156 94 14 56 24 71
CRW_00275 0.86 0.86 0.87 391 1114821 86 15 44 27 66
CRW_00277 0.84 0.84 0.85 379 1110348 89 16 52 21 74
CRW_00278 0.84 0.82 0.86 371 1129827 85 12 46 27 79
CRW_00279 0.82 0.81 0.84 377 1179965 98 18 56 24 87
CRW_00280 0.85 0.85 0.86 384 1117811 93 15 50 28 69
CRW_00281 0.84 0.82 0.85 381 1144895 89 14 51 24 83
CRW_00284 0.84 0.82 0.85 376 1131317 94 16 51 27 80
CRW_00285 0.84 0.83 0.86 380 1117816 91 17 47 27 78
CRW_00289 0.83 0.81 0.85 386 1189199 95 13 55 27 90
CRW_00298 0.58 0.54 0.63 267 1620473 212 31 129 52 227
CRW_00301 0.49 0.46 0.53 240 1762048 265 37 178 50 279
CRW_00306 0.60 0.57 0.63 263 1445430 208 26 131 51 199
CRW_00310 0.55 0.51 0.59 264 1805500 238 32 154 52 257
CRW_00326 0.64 0.60 0.68 299 1627669 193 22 120 51 203
CRW_00330 0.55 0.51 0.60 262 1988577 231 26 150 55 255
CRW_00332 0.51 0.48 0.56 227 1769613 237 20 161 56 250
CRW_00333 0.48 0.43 0.53 220 1892069 260 36 160 64 294
CRW_00345 0.56 0.53 0.60 262 1586434 224 28 147 49 236
CRW_00346 0.59 0.55 0.63 278 1584648 213 32 132 49 223
CRW_00348 0.58 0.54 0.61 272 1615059 225 29 143 53 231
CRW_00358 0.56 0.53 0.60 269 1674914 228 29 153 46 238
CRW_00366 0.60 0.56 0.64 269 1579331 210 25 128 57 213
CRW_00370 0.60 0.57 0.64 288 1640315 211 20 143 48 218
CRW_00371 0.58 0.55 0.60 275 1611455 232 17 163 52 221
CRW_00372 0.59 0.55 0.62 275 1625865 212 23 143 46 223
CRW_00379 0.58 0.52 0.65 277 2126526 213 25 125 63 257
CRW_00386 0.49 0.46 0.53 236 1750812 258 28 180 50 279
CRW_00403 0.53 0.52 0.54 240 1606084 283 31 173 79 224
CRW_00411 0.58 0.54 0.61 269 1615064 222 21 149 52 227
CRW_00414 0.57 0.53 0.62 263 1665801 210 25 136 49 232
CRW_00466 0.85 0.85 0.85 388 1116310 90 13 54 23 70
CRW_00589 0.84 0.82 0.86 367 1094034 98 8 51 39 78
CRW_00590 0.87 0.84 0.89 381 1119329 87 4 42 41 71
CRW_00591 0.85 0.84 0.86 373 1098469 103 7 54 42 73
CRW_00598 0.54 0.51 0.58 250 1665793 234 28 154 52 241
CRW_00758 0.57 0.54 0.61 263 1640333 241 27 143 71 220
CRW_00759 0.56 0.53 0.59 254 1636715 232 18 158 56 227
CRW_00760 0.53 0.49 0.57 239 1638533 247 16 167 64 247
CRW_00772 0.78 0.76 0.80 306 945618 127 7 69 51 98
CRW_00789 0.82 0.80 0.85 357 1137365 108 8 56 44 90
CRW_00795 0.79 0.76 0.82 301 1152552 149 5 63 81 93
CRW_00849 0.80 0.78 0.82 366 1117816 101 14 64 23 104
CRW_00997 0.85 0.84 0.85 389 1135822 85 16 51 18 75
CRW_01153 0.59 0.56 0.63 283 1606076 220 25 144 51 220
CRW_01171 0.52 0.48 0.56 245 1593566 240 31 163 46 261
CRW_01300 0.60 0.55 0.67 283 1693295 193 17 125 51 232
PDB_00703 0.78 0.72 0.84 355 1073423 101 6 61 34 140
PDB_00854 0.75 0.68 0.84 363 1500344 118 10 61 47 172
PDB_01088 0.74 0.65 0.83 357 1471042 115 5 66 44 190
PDB_01103 0.75 0.66 0.85 373 1606088 99 8 59 32 189
PDB_01105 0.75 0.68 0.84 366 1433533 107 4 68 35 174
PDB_01120 0.78 0.72 0.85 378 1204681 101 9 60 32 149
PDB_01273 0.78 0.73 0.84 358 1117834 110 9 59 42 133

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Performance of Carnac(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP 12872
Total TN 104356083
Total FP 2613
Total FP CONTRA 170
Total FP INCONS 1341
Total FP COMP 1102
Total FN 24092
Total Scores
MCC 0.558
Average MCC ± 95% Confidence Intervals 0.553 ± 0.023
Sensitivity 0.348
Positive Predictive Value 0.895
Nr of predictions 77

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.74 0.59 0.94 270 1085313 35 5 13 17 188
CRW_00034 0.56 0.35 0.90 166 1142131 28 4 15 9 308
CRW_00048 0.62 0.43 0.91 202 1170992 29 3 18 8 268
CRW_00054 0.62 0.42 0.91 191 1107607 23 4 14 5 265
CRW_00059 0.64 0.43 0.95 204 1172532 17 3 7 7 269
CRW_00061 0.63 0.42 0.94 199 1181742 19 2 10 7 277
CRW_00068 0.69 0.51 0.94 234 1109056 28 2 13 13 223
CRW_00096 0.62 0.43 0.92 198 1178664 29 0 18 11 267
CRW_00140 0.71 0.53 0.95 246 1136018 21 2 12 7 217
CRW_00141 0.64 0.43 0.93 207 1201802 26 4 12 10 269
CRW_00150 0.66 0.46 0.95 216 1152694 16 3 8 5 250
CRW_00152 0.69 0.52 0.92 244 1180151 26 4 17 5 227
CRW_00166 0.64 0.44 0.93 207 1190974 24 0 15 9 261
CRW_00173 0.56 0.36 0.89 158 1082478 26 2 18 6 287
CRW_00177 0.52 0.32 0.87 149 1178708 29 3 20 6 324
CRW_00196 0.64 0.43 0.96 204 1208022 12 2 7 3 271
CRW_00230 0.66 0.47 0.93 227 1198681 28 3 15 10 251
CRW_00245 0.65 0.45 0.93 205 1106108 20 3 12 5 248
CRW_00248 0.56 0.35 0.91 168 1218956 27 4 13 10 316
CRW_00250 0.68 0.50 0.91 241 1198660 33 4 21 8 237
CRW_00256 0.64 0.43 0.97 200 1192533 11 3 4 4 268
CRW_00270 0.66 0.47 0.93 212 1112057 22 4 13 5 243
CRW_00271 0.62 0.41 0.94 191 1122548 17 3 9 5 271
CRW_00273 0.57 0.35 0.92 156 1085431 16 4 10 2 290
CRW_00275 0.60 0.37 0.95 171 1115091 13 2 7 4 286
CRW_00277 0.64 0.44 0.93 201 1110578 20 3 13 4 252
CRW_00278 0.52 0.29 0.92 130 1130115 15 4 7 4 320
CRW_00279 0.68 0.51 0.92 237 1180158 31 3 18 10 227
CRW_00280 0.66 0.46 0.96 209 1118042 12 1 8 3 244
CRW_00281 0.65 0.45 0.95 209 1145120 17 2 10 5 255
CRW_00284 0.53 0.33 0.87 150 1131587 27 3 20 4 306
CRW_00285 0.62 0.41 0.93 188 1118058 18 2 12 4 270
CRW_00289 0.58 0.41 0.84 194 1189422 41 5 32 4 282
CRW_00298 0.41 0.19 0.86 95 1620790 37 0 15 22 399
CRW_00301 0.46 0.25 0.83 131 1762345 56 0 27 29 388
CRW_00306 0.55 0.32 0.95 146 1445697 38 0 7 31 316
CRW_00310 0.42 0.22 0.81 116 1805806 46 5 23 18 405
CRW_00326 0.45 0.23 0.92 113 1627987 32 1 9 22 389
CRW_00330 0.34 0.17 0.67 89 1988883 69 3 40 26 428
CRW_00332 0.39 0.20 0.76 97 1769893 46 1 30 15 380
CRW_00333 0.35 0.17 0.70 88 1892359 50 4 34 12 426
CRW_00345 0.48 0.29 0.81 145 1586691 63 2 33 28 353
CRW_00346 0.47 0.28 0.79 138 1584915 66 1 36 29 363
CRW_00348 0.40 0.23 0.72 114 1615344 78 4 41 33 389
CRW_00358 0.49 0.25 0.96 129 1675231 29 0 5 24 378
CRW_00366 0.47 0.25 0.87 122 1579613 37 1 17 19 360
CRW_00370 0.47 0.27 0.84 135 1640605 54 1 25 28 371
CRW_00371 0.48 0.29 0.81 143 1611733 59 1 33 25 353
CRW_00372 0.44 0.23 0.84 117 1626166 46 2 21 23 381
CRW_00379 0.49 0.26 0.93 140 2126802 50 1 10 39 394
CRW_00386 0.30 0.13 0.71 67 1751161 53 2 26 25 448
CRW_00403 0.48 0.27 0.83 127 1606375 60 0 26 34 337
CRW_00411 0.39 0.19 0.81 94 1615387 42 0 22 20 402
CRW_00414 0.38 0.19 0.74 96 1666095 60 1 33 26 399
CRW_00466 0.62 0.42 0.91 192 1116554 28 4 15 9 266
CRW_00589 0.58 0.35 0.97 156 1094299 10 0 5 5 289
CRW_00590 0.55 0.33 0.93 148 1119597 15 1 10 4 304
CRW_00591 0.66 0.46 0.93 206 1098682 26 1 14 11 240
CRW_00598 0.42 0.20 0.85 100 1666107 41 0 18 23 391
CRW_00758 0.46 0.26 0.79 127 1640605 57 4 30 23 356
CRW_00759 0.39 0.19 0.79 93 1637028 51 3 21 27 388
CRW_00760 0.45 0.24 0.84 117 1638815 55 0 23 32 369
CRW_00772 0.48 0.30 0.77 122 945842 42 3 33 6 282
CRW_00789 0.61 0.43 0.88 191 1137570 34 1 24 9 256
CRW_00795 0.59 0.38 0.90 150 1152755 40 0 16 24 244
CRW_00849 0.62 0.42 0.92 196 1118046 27 3 15 9 274
CRW_00997 0.60 0.39 0.93 181 1136084 19 3 10 6 283
CRW_01153 0.44 0.25 0.76 126 1606363 56 1 38 17 377
CRW_01171 0.47 0.25 0.90 125 1593866 44 0 14 30 381
CRW_01300 0.47 0.25 0.88 128 1693575 38 0 17 21 387
PDB_00703 0.60 0.40 0.92 196 1073633 28 3 13 12 299
PDB_00854 0.62 0.41 0.95 218 1500548 29 3 9 17 317
PDB_01088 0.59 0.38 0.92 206 1471246 35 2 16 17 341
PDB_01103 0.62 0.40 0.96 226 1606292 20 3 7 10 336
PDB_01105 0.58 0.36 0.94 192 1433767 24 1 11 12 348
PDB_01120 0.62 0.41 0.93 216 1204895 30 4 13 13 311
PDB_01273 0.66 0.48 0.92 234 1118007 37 4 15 18 257

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