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(seed) - 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(seed) & Carnac(20) [.zip] - may take several seconds...


Overview

Metric PETfold_pre2.0(seed) Carnac(20)
MCC 0.760 > 0.558
Average MCC ± 95% Confidence Intervals 0.763 ± 0.022 > 0.553 ± 0.023
Sensitivity 0.730 > 0.348
Positive Predictive Value 0.792 < 0.895
Total TP 26994 > 12872
Total TN 104336380 < 104356083
Total FP 11076 > 2613
Total FP CONTRA 1094 > 170
Total FP INCONS 5998 > 1341
Total FP COMP 3984 > 1102
Total FN 9970 < 24092
P-value 3.56938820447e-08

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Performance plots


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

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

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

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

Total Base Pair Counts
Total TP 26994
Total TN 104336380
Total FP 11076
Total FP CONTRA 1094
Total FP INCONS 5998
Total FP COMP 3984
Total FN 9970
Total Scores
MCC 0.760
Average MCC ± 95% Confidence Intervals 0.763 ± 0.022
Sensitivity 0.730
Positive Predictive Value 0.792
Nr of predictions 77

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2. Individual counts for PETfold_pre2.0(seed) [ 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 0.90 405 1085153 80 10 33 37 53
CRW_00034 0.80 0.78 0.83 369 1141870 113 17 60 36 105
CRW_00048 0.85 0.84 0.87 395 1170759 96 18 43 35 75
CRW_00054 0.86 0.86 0.87 390 1107367 95 16 43 36 66
CRW_00059 0.85 0.83 0.87 392 1172293 95 17 44 34 81
CRW_00061 0.84 0.82 0.86 388 1181504 96 16 45 35 88
CRW_00068 0.86 0.86 0.87 394 1108851 94 17 43 34 63
CRW_00096 0.86 0.84 0.88 392 1178434 98 11 43 44 73
CRW_00140 0.85 0.84 0.86 387 1135829 97 15 47 35 76
CRW_00141 0.85 0.82 0.87 392 1201573 98 16 44 38 84
CRW_00150 0.85 0.83 0.87 385 1152477 92 16 43 33 81
CRW_00152 0.84 0.82 0.86 386 1179969 96 16 45 35 85
CRW_00166 0.86 0.84 0.88 393 1190749 97 11 43 43 75
CRW_00173 0.80 0.79 0.81 353 1082222 118 17 64 37 92
CRW_00177 0.84 0.82 0.86 386 1178430 105 17 47 41 87
CRW_00196 0.83 0.81 0.86 384 1207786 102 15 50 37 91
CRW_00230 0.84 0.82 0.87 392 1198473 97 16 45 36 86
CRW_00245 0.86 0.86 0.87 388 1105880 95 18 42 35 65
CRW_00248 0.83 0.80 0.86 388 1218691 98 16 46 36 96
CRW_00250 0.84 0.82 0.87 391 1198474 97 16 45 36 87
CRW_00256 0.85 0.82 0.87 386 1192295 93 16 43 34 82
CRW_00270 0.87 0.86 0.87 391 1111838 94 15 42 37 64
CRW_00271 0.83 0.82 0.85 378 1122307 105 14 52 39 84
CRW_00273 0.86 0.85 0.86 380 1085161 98 14 46 38 66
CRW_00275 0.86 0.85 0.87 390 1114823 98 15 43 40 67
CRW_00277 0.84 0.83 0.85 377 1110354 101 16 48 37 76
CRW_00278 0.84 0.82 0.85 369 1129823 106 15 49 42 81
CRW_00279 0.85 0.83 0.86 385 1179970 103 16 45 42 79
CRW_00280 0.84 0.83 0.85 377 1117815 109 16 52 41 76
CRW_00281 0.85 0.84 0.87 388 1144894 97 16 43 38 76
CRW_00284 0.83 0.82 0.84 372 1131319 111 16 53 42 84
CRW_00285 0.84 0.82 0.85 377 1117816 104 17 50 37 81
CRW_00289 0.82 0.80 0.84 382 1189200 109 16 55 38 94
CRW_00298 0.66 0.63 0.69 310 1620452 212 16 122 74 184
CRW_00301 0.63 0.59 0.67 307 1762046 213 15 135 63 212
CRW_00306 0.68 0.66 0.70 305 1445417 186 15 113 58 157
CRW_00310 0.63 0.59 0.68 305 1805503 209 14 128 67 216
CRW_00326 0.66 0.63 0.69 315 1627654 205 15 126 64 187
CRW_00330 0.64 0.59 0.69 307 1988567 210 13 128 69 210
CRW_00332 0.60 0.56 0.63 269 1769595 236 16 141 79 208
CRW_00333 0.58 0.52 0.64 269 1892065 217 19 132 66 245
CRW_00345 0.64 0.61 0.67 305 1586418 211 15 133 63 193
CRW_00346 0.65 0.61 0.69 308 1584644 204 15 123 66 193
CRW_00348 0.65 0.62 0.68 312 1615046 210 15 130 65 191
CRW_00358 0.64 0.60 0.67 306 1674911 213 16 132 65 201
CRW_00366 0.65 0.62 0.68 300 1579311 211 15 127 69 182
CRW_00370 0.65 0.62 0.69 313 1640313 205 15 125 65 193
CRW_00371 0.68 0.65 0.71 322 1611455 199 13 120 66 174
CRW_00372 0.64 0.61 0.67 306 1625847 221 14 139 68 192
CRW_00379 0.60 0.54 0.66 286 2126521 223 18 128 77 248
CRW_00386 0.61 0.58 0.65 297 1750802 227 16 141 70 218
CRW_00403 0.68 0.66 0.70 306 1606090 215 15 117 83 158
CRW_00411 0.67 0.64 0.71 318 1615053 200 15 117 68 178
CRW_00414 0.64 0.61 0.67 303 1665770 223 20 132 71 192
CRW_00466 0.86 0.85 0.87 391 1116315 99 14 45 40 67
CRW_00589 0.87 0.84 0.89 376 1094037 99 6 41 52 69
CRW_00590 0.87 0.84 0.89 381 1119327 104 6 42 56 71
CRW_00591 0.87 0.86 0.89 382 1098473 103 6 42 55 64
CRW_00598 0.63 0.60 0.66 294 1665777 224 19 135 70 197
CRW_00758 0.64 0.61 0.67 294 1640327 224 15 130 79 189
CRW_00759 0.65 0.62 0.68 297 1636709 218 15 124 79 184
CRW_00760 0.63 0.59 0.66 287 1638522 227 17 129 81 199
CRW_00772 0.79 0.76 0.81 309 945618 130 6 67 57 95
CRW_00789 0.83 0.81 0.86 362 1137365 112 11 48 53 85
CRW_00795 0.79 0.76 0.82 299 1152557 159 6 59 94 95
CRW_00849 0.79 0.76 0.81 359 1117819 116 16 66 34 111
CRW_00997 0.86 0.85 0.87 395 1135823 93 17 43 33 69
CRW_01153 0.61 0.58 0.64 294 1606070 223 18 146 59 209
CRW_01171 0.63 0.60 0.67 304 1593548 214 15 138 61 202
CRW_01300 0.62 0.59 0.66 302 1693261 218 17 140 61 213
PDB_00703 0.79 0.73 0.86 361 1073423 107 9 52 46 134
PDB_00854 0.76 0.68 0.86 364 1500354 120 9 51 60 171
PDB_01088 0.75 0.67 0.85 365 1471040 119 5 60 54 182
PDB_01103 0.76 0.67 0.86 376 1606090 108 8 54 46 186
PDB_01105 0.77 0.70 0.86 376 1433534 108 3 58 47 164
PDB_01120 0.80 0.73 0.86 387 1204680 102 10 51 41 140
PDB_01273 0.80 0.75 0.86 368 1117832 112 8 52 52 123

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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.