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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 Carnac(20) - scored lower in this pairwise comparison

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


Overview

Metric CentroidAlifold(20) Carnac(20)
MCC 0.726 > 0.558
Average MCC ± 95% Confidence Intervals 0.718 ± 0.036 > 0.553 ± 0.023
Sensitivity 0.614 > 0.348
Positive Predictive Value 0.860 < 0.895
Total TP 22679 > 12872
Total TN 104344087 < 104356083
Total FP 5560 > 2613
Total FP CONTRA 629 > 170
Total FP INCONS 3071 > 1341
Total FP COMP 1860 > 1102
Total FN 14285 < 24092
P-value 3.56938820447e-08

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Performance plots


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

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