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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 MaxExpect - scored lower in this pairwise comparison

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


Overview

Metric CentroidAlifold(20) MaxExpect
MCC 0.726 > 0.415
Average MCC ± 95% Confidence Intervals 0.718 ± 0.036 > 0.416 ± 0.027
Sensitivity 0.614 > 0.406
Positive Predictive Value 0.860 > 0.424
Total TP 22679 > 15020
Total TN 104344087 > 104335019
Total FP 5560 < 22934
Total FP CONTRA 629 < 3099
Total FP INCONS 3071 < 17328
Total FP COMP 1860 < 2507
Total FN 14285 < 21944
P-value 3.56938820447e-08

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Performance plots


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

  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 MaxExpect).

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

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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 MaxExpect - scored lower in this pairwise comparison

1. Total counts & total scores for MaxExpect

Total Base Pair Counts
Total TP 15020
Total TN 104335019
Total FP 22934
Total FP CONTRA 3099
Total FP INCONS 17328
Total FP COMP 2507
Total FN 21944
Total Scores
MCC 0.415
Average MCC ± 95% Confidence Intervals 0.416 ± 0.027
Sensitivity 0.406
Positive Predictive Value 0.424
Nr of predictions 77

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.71 0.70 0.71 320 1085152 169 17 112 40 138
CRW_00034 0.66 0.65 0.66 310 1141844 191 28 134 29 164
CRW_00048 0.52 0.48 0.57 226 1170816 189 20 153 16 244
CRW_00054 0.43 0.42 0.44 192 1107377 261 23 224 14 264
CRW_00059 0.51 0.49 0.54 232 1172316 212 16 182 14 241
CRW_00061 0.44 0.43 0.45 203 1181497 266 35 218 13 273
CRW_00068 0.44 0.43 0.45 197 1108869 251 32 207 12 260
CRW_00096 0.49 0.47 0.52 220 1178453 229 21 186 22 245
CRW_00140 0.43 0.42 0.44 193 1135835 265 20 230 15 270
CRW_00141 0.54 0.53 0.55 254 1201566 230 30 175 25 222
CRW_00150 0.44 0.43 0.46 202 1152479 257 24 216 17 264
CRW_00152 0.58 0.55 0.60 259 1179986 190 37 134 19 212
CRW_00166 0.43 0.41 0.46 192 1190777 241 18 209 14 276
CRW_00173 0.26 0.26 0.27 115 1082230 324 28 283 13 330
CRW_00177 0.48 0.47 0.50 221 1178440 239 26 193 20 252
CRW_00196 0.50 0.49 0.51 233 1207782 238 32 188 18 242
CRW_00230 0.58 0.55 0.60 263 1198489 199 15 159 25 215
CRW_00245 0.42 0.41 0.43 186 1105895 262 25 222 15 267
CRW_00248 0.51 0.51 0.51 248 1218656 263 29 208 26 236
CRW_00250 0.51 0.50 0.51 241 1198458 244 44 183 17 237
CRW_00256 0.40 0.39 0.41 182 1192293 285 38 227 20 286
CRW_00270 0.54 0.54 0.55 244 1111842 223 23 177 23 211
CRW_00271 0.33 0.32 0.34 146 1122327 292 34 244 14 316
CRW_00273 0.42 0.40 0.45 180 1085197 237 27 197 13 266
CRW_00275 0.61 0.60 0.62 273 1114831 186 26 141 19 184
CRW_00277 0.35 0.33 0.37 148 1110390 267 37 220 10 305
CRW_00278 0.39 0.36 0.42 160 1129876 240 22 198 20 290
CRW_00279 0.54 0.53 0.56 244 1179977 213 26 169 18 220
CRW_00280 0.36 0.35 0.37 157 1117836 279 37 230 12 296
CRW_00281 0.59 0.58 0.60 270 1144891 201 25 155 21 194
CRW_00284 0.38 0.35 0.41 159 1131368 249 21 212 16 297
CRW_00285 0.56 0.54 0.58 246 1117835 199 26 153 20 212
CRW_00289 0.48 0.46 0.50 218 1189213 245 32 190 23 258
CRW_00298 0.24 0.25 0.24 123 1620380 438 79 318 41 371
CRW_00301 0.35 0.35 0.35 180 1761991 393 60 272 61 339
CRW_00306 0.18 0.19 0.18 86 1445370 462 62 332 68 376
CRW_00310 0.30 0.30 0.30 157 1805427 422 63 303 56 364
CRW_00326 0.41 0.41 0.42 205 1627618 330 55 232 43 297
CRW_00330 0.33 0.33 0.32 172 1988480 429 65 298 66 345
CRW_00332 0.18 0.18 0.17 87 1769512 473 87 335 51 390
CRW_00333 0.33 0.32 0.35 166 1892006 380 65 248 67 348
CRW_00345 0.35 0.35 0.36 174 1586388 361 52 257 52 324
CRW_00346 0.37 0.38 0.37 188 1584581 361 62 259 40 313
CRW_00348 0.31 0.30 0.33 151 1615043 353 51 258 44 352
CRW_00358 0.41 0.41 0.42 206 1674869 336 56 234 46 301
CRW_00366 0.27 0.28 0.26 134 1579236 421 78 305 38 348
CRW_00370 0.30 0.30 0.30 151 1640256 403 77 282 44 355
CRW_00371 0.40 0.39 0.42 192 1611452 316 45 221 50 304
CRW_00372 0.28 0.28 0.27 139 1625798 414 78 291 45 359
CRW_00379 0.44 0.44 0.43 234 2126414 384 57 248 79 300
CRW_00386 0.26 0.27 0.25 138 1750712 440 78 328 34 377
CRW_00403 0.31 0.31 0.31 144 1606062 415 58 264 93 320
CRW_00411 0.33 0.33 0.34 163 1615021 361 68 251 42 333
CRW_00414 0.30 0.31 0.30 153 1665712 421 60 300 61 342
CRW_00466 0.61 0.60 0.62 273 1116325 188 25 142 21 185
CRW_00589 0.32 0.31 0.34 136 1094057 285 28 239 18 309
CRW_00590 0.40 0.37 0.43 169 1119363 246 23 201 22 283
CRW_00591 0.44 0.43 0.44 194 1098463 264 36 210 18 252
CRW_00598 0.38 0.39 0.38 190 1665724 360 63 248 49 301
CRW_00758 0.33 0.32 0.34 155 1640308 356 41 262 53 328
CRW_00759 0.31 0.31 0.30 151 1636649 407 59 286 62 330
CRW_00760 0.29 0.29 0.28 143 1638449 415 65 298 52 343
CRW_00772 0.22 0.21 0.23 85 945632 297 29 254 14 319
CRW_00789 0.37 0.37 0.38 165 1137350 293 39 232 22 282
CRW_00795 0.35 0.35 0.35 138 1152523 307 34 226 47 256
CRW_00849 0.58 0.58 0.59 271 1117802 215 14 173 28 199
CRW_00997 0.44 0.42 0.45 197 1135837 260 32 212 16 267
CRW_01153 0.30 0.30 0.30 151 1606020 397 56 301 40 352
CRW_01171 0.33 0.33 0.34 167 1593511 375 57 270 48 339
CRW_01300 0.35 0.34 0.35 177 1693219 370 60 264 46 338
PDB_00703 0.57 0.52 0.62 259 1073427 187 20 139 28 236
PDB_00854 0.58 0.56 0.60 298 1500283 247 21 176 50 237
PDB_01088 0.33 0.32 0.35 176 1470965 353 46 283 24 371
PDB_01103 0.63 0.60 0.67 337 1606027 197 18 146 33 225
PDB_01105 0.57 0.54 0.60 289 1433488 229 24 170 35 251
PDB_01120 0.43 0.40 0.46 211 1204672 264 28 217 19 316
PDB_01273 0.45 0.43 0.46 211 1117804 273 31 214 28 280

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