CompaRNA - on-line benchmarks of RNA structure prediction methods
Home

Methods
Datasets
Rankings
RNA 2D Atlas

Help
FAQ

Contact us
RSS feeds
Twitter

Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric PETfold_pre2.0(20) Contrafold
MCC 0.728 > 0.477
Average MCC ± 95% Confidence Intervals 0.730 ± 0.030 > 0.480 ± 0.027
Sensitivity 0.697 > 0.461
Positive Predictive Value 0.760 > 0.494
Total TP 25763 > 17036
Total TN 104336584 > 104335974
Total FP 11045 < 20448
Total FP CONTRA 1367 < 2637
Total FP INCONS 6752 < 14819
Total FP COMP 2926 < 2992
Total FN 11201 < 19928
P-value 3.56938820447e-08

^top




Performance plots


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

  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 Contrafold).

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

^top





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

^top



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

^top



Performance of Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP 17036
Total TN 104335974
Total FP 20448
Total FP CONTRA 2637
Total FP INCONS 14819
Total FP COMP 2992
Total FN 19928
Total Scores
MCC 0.477
Average MCC ± 95% Confidence Intervals 0.480 ± 0.027
Sensitivity 0.461
Positive Predictive Value 0.494
Nr of predictions 77

^top



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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.77 0.77 0.78 351 1085153 140 12 85 43 107
CRW_00034 0.68 0.68 0.68 320 1141844 188 22 130 36 154
CRW_00048 0.60 0.57 0.64 268 1170795 174 25 127 22 202
CRW_00054 0.54 0.52 0.56 237 1107395 202 25 159 18 219
CRW_00059 0.64 0.60 0.67 286 1172318 164 20 122 22 187
CRW_00061 0.59 0.58 0.61 274 1181504 188 29 146 13 202
CRW_00068 0.51 0.51 0.53 231 1108865 226 32 177 17 226
CRW_00096 0.55 0.53 0.57 245 1178450 213 19 166 28 220
CRW_00140 0.56 0.52 0.61 243 1135878 175 14 143 18 220
CRW_00141 0.62 0.60 0.64 287 1201577 192 19 142 31 189
CRW_00150 0.55 0.51 0.59 237 1152519 185 22 143 20 229
CRW_00152 0.53 0.49 0.57 233 1180006 196 22 155 19 238
CRW_00166 0.62 0.59 0.64 277 1190763 182 19 137 26 191
CRW_00173 0.34 0.34 0.35 150 1082228 288 32 246 10 295
CRW_00177 0.50 0.48 0.52 228 1178444 227 20 188 19 245
CRW_00196 0.57 0.55 0.59 259 1207798 197 27 151 19 216
CRW_00230 0.54 0.52 0.56 250 1198476 220 27 173 20 228
CRW_00245 0.53 0.51 0.55 229 1105912 212 23 164 25 224
CRW_00248 0.64 0.62 0.66 301 1218683 200 21 136 43 183
CRW_00250 0.58 0.56 0.61 267 1198490 184 24 145 15 211
CRW_00256 0.47 0.44 0.50 206 1192327 232 26 181 25 262
CRW_00270 0.66 0.63 0.69 286 1111874 157 20 106 31 169
CRW_00271 0.51 0.48 0.53 221 1122337 215 30 163 22 241
CRW_00273 0.47 0.46 0.49 203 1085190 233 20 188 25 243
CRW_00275 0.61 0.59 0.63 271 1114843 186 19 138 29 186
CRW_00277 0.44 0.40 0.49 182 1110423 203 23 167 13 271
CRW_00278 0.44 0.42 0.47 190 1129849 240 28 189 23 260
CRW_00279 0.60 0.56 0.64 262 1180004 173 25 125 23 202
CRW_00280 0.55 0.51 0.60 232 1117873 173 15 140 18 221
CRW_00281 0.64 0.62 0.65 288 1144901 182 17 135 30 176
CRW_00284 0.51 0.47 0.56 216 1131371 196 24 149 23 240
CRW_00285 0.66 0.63 0.68 289 1117836 159 19 116 24 169
CRW_00289 0.60 0.57 0.63 270 1189221 197 21 141 35 206
CRW_00298 0.25 0.25 0.25 122 1620403 431 72 303 56 372
CRW_00301 0.43 0.40 0.45 210 1762038 324 41 214 69 309
CRW_00306 0.28 0.28 0.29 129 1445402 388 63 256 69 333
CRW_00310 0.36 0.35 0.37 184 1805456 377 53 257 67 337
CRW_00326 0.50 0.49 0.51 246 1627630 284 52 182 50 256
CRW_00330 0.33 0.32 0.33 166 1988512 422 56 281 85 351
CRW_00332 0.26 0.26 0.26 122 1769544 429 70 285 74 355
CRW_00333 0.38 0.36 0.41 183 1892040 342 42 220 80 331
CRW_00345 0.39 0.40 0.39 197 1586366 355 58 250 47 301
CRW_00346 0.40 0.40 0.39 202 1584577 358 54 257 47 299
CRW_00348 0.35 0.34 0.36 170 1615029 355 51 253 51 333
CRW_00358 0.39 0.40 0.38 202 1674827 390 57 279 54 305
CRW_00366 0.33 0.33 0.33 157 1579284 361 57 255 49 325
CRW_00370 0.37 0.37 0.37 189 1640256 363 64 257 42 317
CRW_00371 0.44 0.41 0.46 205 1611467 295 42 196 57 291
CRW_00372 0.41 0.40 0.42 198 1625830 342 48 230 64 300
CRW_00379 0.43 0.42 0.44 223 2126443 372 38 249 85 311
CRW_00386 0.28 0.30 0.27 152 1750697 447 70 337 40 363
CRW_00403 0.28 0.28 0.28 131 1606062 404 68 267 69 333
CRW_00411 0.39 0.36 0.42 181 1615070 306 41 211 54 315
CRW_00414 0.36 0.37 0.36 181 1665721 382 54 269 59 314
CRW_00466 0.70 0.68 0.73 312 1116336 148 19 98 31 146
CRW_00589 0.33 0.30 0.36 134 1094090 257 24 212 21 311
CRW_00590 0.36 0.35 0.38 157 1119345 281 41 213 27 295
CRW_00591 0.62 0.60 0.65 268 1098489 182 28 118 36 178
CRW_00598 0.39 0.39 0.40 193 1665739 354 59 234 61 298
CRW_00758 0.35 0.35 0.35 170 1640283 375 51 262 62 313
CRW_00759 0.31 0.30 0.32 145 1636697 372 51 252 69 336
CRW_00760 0.37 0.36 0.37 176 1638485 358 65 229 64 310
CRW_00772 0.40 0.37 0.44 148 945666 215 18 168 29 256
CRW_00789 0.48 0.44 0.53 196 1137416 209 14 160 35 251
CRW_00795 0.35 0.33 0.38 131 1152575 263 22 193 48 263
CRW_00849 0.57 0.56 0.57 265 1117797 226 19 179 28 205
CRW_00997 0.62 0.60 0.64 280 1135838 187 19 141 27 184
CRW_01153 0.39 0.39 0.40 194 1606043 347 52 239 56 309
CRW_01171 0.45 0.44 0.47 221 1593534 302 49 201 52 285
CRW_01300 0.38 0.37 0.38 193 1693217 355 53 257 45 322
PDB_00703 0.53 0.50 0.56 246 1073403 229 19 177 33 249
PDB_00854 0.50 0.49 0.52 264 1500266 296 25 223 48 271
PDB_01088 0.46 0.43 0.49 236 1470988 271 34 212 25 311
PDB_01103 0.55 0.54 0.56 301 1605989 279 31 207 41 261
PDB_01105 0.58 0.56 0.60 303 1433467 242 16 185 41 237
PDB_01120 0.49 0.44 0.55 232 1204703 216 20 173 23 295
PDB_01273 0.49 0.47 0.51 232 1117807 258 16 205 37 259

^top


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