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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 RSpredict(20) - scored lower in this pairwise comparison

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


Overview

Metric PETfold_pre2.0(20) RSpredict(20)
MCC 0.728 > 0.012
Average MCC ± 95% Confidence Intervals 0.730 ± 0.030 > 0.013 ± 0.003
Sensitivity 0.697 > 0.012
Positive Predictive Value 0.760 > 0.014
Total TP 25763 > 436
Total TN 104336584 < 104338716
Total FP 11045 < 32060
Total FP CONTRA 1367 < 4727
Total FP INCONS 6752 < 26587
Total FP COMP 2926 > 746
Total FN 11201 < 36528
P-value 3.56938820447e-08

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Performance plots


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

  3. Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(20) and RSpredict(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 RSpredict(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 RSpredict(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP 436
Total TN 104338716
Total FP 32060
Total FP CONTRA 4727
Total FP INCONS 26587
Total FP COMP 746
Total FN 36528
Total Scores
MCC 0.012
Average MCC ± 95% Confidence Intervals 0.013 ± 0.003
Sensitivity 0.012
Positive Predictive Value 0.014
Nr of predictions 77

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024 0.00 0.00 0.00 0 1085139 462 69 393 0 458
CRW_00034 0.00 0.00 0.00 0 1141928 389 59 329 1 474
CRW_00048 0.00 0.00 0.00 0 1170785 432 69 361 2 470
CRW_00054 0.03 0.03 0.03 14 1107398 407 51 353 3 442
CRW_00059 0.02 0.02 0.02 9 1172337 401 54 346 1 464
CRW_00061 0.02 0.02 0.02 9 1181530 414 57 357 0 467
CRW_00068 0.02 0.02 0.02 9 1108900 397 50 346 1 448
CRW_00096 0.00 0.00 0.00 0 1178457 425 69 354 2 465
CRW_00140 0.02 0.02 0.02 10 1135850 420 52 366 2 453
CRW_00141 0.00 0.00 0.00 0 1201601 424 53 371 0 476
CRW_00150 0.00 0.00 0.00 1 1152501 423 55 364 4 465
CRW_00152 0.00 0.00 0.00 0 1179985 433 63 368 2 471
CRW_00166 0.00 0.00 0.00 0 1190754 442 64 378 0 468
CRW_00173 0.01 0.01 0.01 3 1082257 404 52 344 8 442
CRW_00177 0.01 0.01 0.01 4 1178459 419 57 360 2 469
CRW_00196 0.00 0.00 0.00 0 1207806 431 77 352 2 475
CRW_00230 0.02 0.02 0.02 9 1198500 417 63 354 0 469
CRW_00245 0.02 0.02 0.03 10 1105929 391 75 314 2 443
CRW_00248 0.00 0.00 0.00 0 1218696 448 74 371 3 484
CRW_00250 0.00 0.00 0.00 0 1198499 431 60 367 4 478
CRW_00256 0.00 0.00 0.00 0 1192334 416 54 352 10 468
CRW_00270 0.02 0.02 0.02 10 1111874 406 58 344 4 445
CRW_00271 0.03 0.03 0.03 12 1122350 389 52 337 0 450
CRW_00273 0.02 0.02 0.02 9 1085210 383 50 332 1 437
CRW_00275 0.02 0.02 0.02 9 1114870 392 54 338 0 448
CRW_00277 0.03 0.03 0.03 12 1110392 394 69 322 3 441
CRW_00278 0.04 0.04 0.05 19 1129855 384 58 324 2 431
CRW_00279 0.00 0.00 0.00 0 1180000 419 62 354 3 464
CRW_00280 0.02 0.02 0.02 9 1117843 408 79 329 0 444
CRW_00281 0.02 0.02 0.02 10 1144926 405 59 346 0 454
CRW_00284 0.02 0.02 0.02 10 1131353 400 72 325 3 446
CRW_00285 0.02 0.02 0.02 9 1117861 393 58 332 3 449
CRW_00289 0.09 0.09 0.10 43 1189225 390 55 330 5 433
CRW_00298 0.01 0.01 0.01 3 1620508 410 63 326 21 491
CRW_00301 0.02 0.02 0.02 8 1762034 472 82 379 11 511
CRW_00306 0.00 0.00 0.00 0 1445474 405 54 322 29 462
CRW_00310 0.02 0.02 0.02 8 1805520 442 63 359 20 513
CRW_00326 0.02 0.02 0.02 8 1627675 437 70 357 10 494
CRW_00330 0.02 0.02 0.02 8 1988575 477 82 350 45 509
CRW_00332 0.01 0.01 0.01 3 1769654 389 59 305 25 474
CRW_00333 0.00 0.00 0.00 1 1892051 454 80 353 21 513
CRW_00345 0.02 0.02 0.02 8 1586488 384 57 318 9 490
CRW_00346 0.01 0.01 0.01 4 1584683 432 63 340 29 497
CRW_00348 0.00 0.00 0.00 0 1615104 410 69 330 11 503
CRW_00358 0.00 0.00 0.00 0 1674979 406 62 324 20 507
CRW_00366 0.01 0.01 0.01 4 1579393 371 66 290 15 478
CRW_00370 0.02 0.02 0.02 10 1640309 469 52 395 22 496
CRW_00371 0.02 0.02 0.02 8 1611495 424 63 344 17 488
CRW_00372 0.02 0.02 0.02 8 1625926 390 51 321 18 490
CRW_00379 0.00 0.00 0.00 0 2126541 465 66 346 53 534
CRW_00386 0.02 0.02 0.02 8 1750835 427 65 348 14 507
CRW_00403 0.00 0.00 0.00 0 1606168 385 68 292 25 464
CRW_00411 0.00 0.00 0.00 0 1615135 382 74 294 14 496
CRW_00414 0.01 0.01 0.01 3 1665773 466 78 371 17 492
CRW_00466 0.02 0.02 0.02 9 1116356 402 42 358 2 449
CRW_00589 0.02 0.02 0.02 9 1094068 388 55 328 5 436
CRW_00590 0.02 0.02 0.02 10 1119344 403 68 334 1 442
CRW_00591 0.02 0.02 0.02 10 1098502 403 46 345 12 436
CRW_00598 0.00 0.00 0.00 0 1665800 449 72 353 24 491
CRW_00758 0.00 0.00 0.00 0 1640340 444 79 347 18 483
CRW_00759 0.02 0.02 0.02 9 1636732 429 64 340 25 472
CRW_00760 0.00 0.00 0.00 0 1638553 425 77 325 23 486
CRW_00772 0.00 0.00 0.01 2 945654 349 60 284 5 402
CRW_00789 0.02 0.02 0.02 9 1137394 389 58 325 6 438
CRW_00795 0.04 0.04 0.04 16 1152547 382 70 288 24 378
CRW_00849 0.02 0.02 0.02 9 1117851 401 56 344 1 461
CRW_00997 0.02 0.02 0.02 9 1135858 413 68 343 2 455
CRW_01153 0.00 0.00 0.00 0 1606093 451 64 371 16 503
CRW_01171 0.02 0.01 0.02 7 1593610 403 61 327 15 499
CRW_01300 0.00 0.00 0.00 0 1693285 445 62 373 10 515
PDB_00703 0.02 0.02 0.02 10 1073431 406 37 367 2 485
PDB_00854 0.00 0.00 0.00 0 1500347 438 69 362 7 535
PDB_01088 0.00 0.00 0.00 0 1471042 432 49 379 4 547
PDB_01103 0.00 0.00 0.00 0 1606098 437 45 385 7 562
PDB_01105 0.01 0.01 0.01 3 1433548 430 47 373 10 537
PDB_01120 0.00 0.00 0.00 0 1204692 440 41 395 4 527
PDB_01273 0.00 0.00 0.00 2 1117847 415 47 364 4 489

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