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Table of contents:

  1. Overview

  2. Performance Plots

  3. Performance of Sfold - scored higher in this pairwise comparison

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

  5. Compile and download dataset for Sfold & RNAwolf [.zip] - may take several seconds...


Overview

Metric Sfold RNAwolf
MCC 0.374 > 0.199
Average MCC ± 95% Confidence Intervals 0.395 ± 0.032 > 0.215 ± 0.027
Sensitivity 0.321 > 0.212
Positive Predictive Value 0.436 > 0.188
Total TP 6625 > 4369
Total TN 45329871 > 45321852
Total FP 12294 < 24745
Total FP CONTRA 1666 < 3879
Total FP INCONS 6912 < 14974
Total FP COMP 3716 < 5892
Total FN 13988 < 16244
P-value 3.56938820447e-08

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Performance plots


  1. Comparison of performance of Sfold and RNAwolf. 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 Sfold and RNAwolf).

  2. Comparison of average Matthews Correlation Coefficients (MCCs) for Sfold and RNAwolf. 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 Sfold and RNAwolf).

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Performance of Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP 6625
Total TN 45329871
Total FP 12294
Total FP CONTRA 1666
Total FP INCONS 6912
Total FP COMP 3716
Total FN 13988
Total Scores
MCC 0.374
Average MCC ± 95% Confidence Intervals 0.395 ± 0.032
Sensitivity 0.321
Positive Predictive Value 0.436
Nr of predictions 88

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00002 - 0.55 0.46 0.67 122 408877 74 22 39 13 142
CRW_00417 - 0.38 0.32 0.45 85 458216 111 14 88 9 177
CRW_00418 - 0.28 0.22 0.36 58 441170 106 13 89 4 202
CRW_00419 - 0.17 0.12 0.24 32 464034 104 10 90 4 233
CRW_00421 - 0.56 0.37 0.83 99 463084 32 1 19 12 167
CRW_00422 - 0.41 0.38 0.45 101 455309 146 20 105 21 162
CRW_00424 - 0.39 0.38 0.41 137 789065 212 14 180 18 226
CRW_00426 - 0.51 0.42 0.61 111 457264 77 8 63 6 154
CRW_00427 - 0.26 0.21 0.33 54 454417 116 25 85 6 207
CRW_00428 - 0.40 0.35 0.47 90 465903 112 17 85 10 170
CRW_00430 - 0.35 0.24 0.52 63 456369 64 11 47 6 203
CRW_00433 - 0.40 0.27 0.59 70 467910 52 3 45 4 193
CRW_00434 - 0.25 0.22 0.28 58 457241 157 8 139 10 205
CRW_00435 - 0.38 0.33 0.43 88 451518 122 15 104 3 177
CRW_00437 - 0.26 0.21 0.33 55 456321 116 14 100 2 205
CRW_00438 - 0.35 0.33 0.38 88 454349 154 19 125 10 180
CRW_00441 - 0.22 0.17 0.28 44 454424 117 13 100 4 218
CRW_00442 - 0.40 0.35 0.46 91 453428 118 21 88 9 170
CRW_00443 - 0.38 0.31 0.48 80 456322 102 10 78 14 180
CRW_00444 - 0.24 0.20 0.30 53 459183 130 15 110 5 210
CRW_00445 - 0.32 0.26 0.38 70 458220 118 17 96 5 195
CRW_00446 - 0.44 0.35 0.55 94 468826 82 6 70 6 171
CRW_00447 - 0.35 0.28 0.43 72 452509 108 10 85 13 188
CRW_00448 - 0.34 0.30 0.40 78 457250 129 22 96 11 183
CRW_00449 - 0.33 0.27 0.41 69 444929 98 12 86 0 191
CRW_00450 - 0.34 0.28 0.42 74 458226 117 12 91 14 188
CRW_00451 - 0.21 0.19 0.23 50 457228 180 22 146 12 214
CRW_00452 - 0.31 0.26 0.39 67 453454 122 14 93 15 195
CRW_00453 - 0.27 0.22 0.34 58 452503 121 20 95 6 203
CRW_00456 - 0.45 0.37 0.54 98 470753 93 13 71 9 167
CRW_00457 - 0.53 0.41 0.69 108 467872 63 6 42 15 156
CRW_00458 - 0.48 0.41 0.56 108 464937 94 13 72 9 156
CRW_00459 - 0.47 0.37 0.58 98 462073 86 11 59 16 165
CRW_00462 - 0.33 0.28 0.40 72 458225 122 11 95 16 189
CRW_00463 - 0.41 0.31 0.54 78 445896 77 11 55 11 176
CRW_00464 - 0.45 0.37 0.54 98 462061 92 9 73 10 166
CRW_00530 - 0.28 0.26 0.29 71 534854 184 48 122 14 197
CRW_00532 - 0.19 0.15 0.24 40 579258 133 33 95 5 225
CRW_00533 - 0.38 0.25 0.57 55 453532 52 8 33 11 164
CRW_00538 - 0.28 0.24 0.32 73 811950 166 43 109 14 227
CRW_00604 - 0.55 0.57 0.53 46 411692 193 15 25 153 35
CRW_00606 - 0.76 0.65 0.88 60 559085 217 0 8 209 32
CRW_00607 - 0.62 0.52 0.74 40 536076 246 6 8 232 37
CRW_00615 - 0.52 0.55 0.48 45 553785 257 18 30 209 37
CRW_00617 - 0.53 0.45 0.63 29 426380 204 1 16 187 35
CRW_00678 - 0.74 0.59 0.93 71 666359 115 0 5 110 50
CRW_00680 - 0.64 0.63 0.65 77 516518 179 7 34 138 45
CRW_00683 - 0.56 0.47 0.66 63 460225 158 7 25 126 72
CRW_00684 - 0.43 0.44 0.42 60 612029 233 30 52 151 75
CRW_00702 - 0.62 0.60 0.63 45 357364 124 6 20 98 30
CRW_00704 - 0.87 0.86 0.88 81 386668 181 4 7 170 13
CRW_00706 - 0.61 0.54 0.68 32 695563 227 1 14 212 27
CRW_00713 - 0.60 0.57 0.63 58 731353 257 7 27 223 43
CRW_00730 - 0.52 0.56 0.48 90 338888 158 29 69 60 71
CRW_00734 - 0.19 0.25 0.15 27 536980 230 87 72 71 83
CRW_00735 - 0.30 0.40 0.22 49 677806 231 102 73 56 72
CRW_00740 - 0.00 0.00 0.00 0 489455 174 39 61 74 113
CRW_00746 - 0.53 0.49 0.57 107 550538 129 17 63 49 112
CRW_00750 - 0.29 0.31 0.27 49 709655 239 47 85 107 111
CRW_00751 - 0.57 0.59 0.55 105 489365 137 32 53 52 73
CRW_00753 - 0.18 0.19 0.18 33 489369 220 39 114 67 145
CRW_00757 - 0.14 0.15 0.14 19 415279 196 35 83 78 107
CRW_00765 - 0.52 0.47 0.59 120 452472 95 9 75 11 137
CRW_00766 - 0.31 0.22 0.44 53 440271 79 13 54 12 187
CRW_00768 - 0.49 0.36 0.69 92 471772 55 2 40 13 167
CRW_00769 - 0.52 0.41 0.65 104 451564 69 12 45 12 148
CRW_00773 - 0.53 0.48 0.59 124 451516 97 20 65 12 135
CRW_00774 - 0.33 0.27 0.39 72 488380 135 11 103 21 191
CRW_00777 - 0.30 0.28 0.33 84 719148 191 28 140 23 220
CRW_00780 - 0.34 0.29 0.39 75 475607 124 19 99 6 180
CRW_00783 - 0.38 0.22 0.68 56 453546 31 3 23 5 203
CRW_00784 - 0.25 0.22 0.28 57 456289 157 29 115 13 205
CRW_00785 - 0.38 0.29 0.51 73 452532 77 12 59 6 180
CRW_00787 - 0.32 0.28 0.37 85 646722 155 20 126 9 221
CRW_00794 - 0.24 0.22 0.25 55 434562 180 12 149 19 191
CRW_00796 - 0.29 0.23 0.35 55 384845 117 15 88 14 180
CRW_00797 - 0.29 0.27 0.33 91 692975 208 24 163 21 251
CRW_00801 - 0.47 0.43 0.52 108 438307 114 27 74 13 141
CRW_00802 - 0.30 0.25 0.36 62 460150 118 24 84 10 191
CRW_00813 - 0.16 0.18 0.15 24 530800 277 43 98 136 109
CRW_01186 - 0.28 0.21 0.38 82 836356 142 22 111 9 304
CRW_01250 - 0.32 0.27 0.39 101 781618 162 24 132 6 277
CRW_01266 - 0.37 0.32 0.43 123 818277 173 25 135 13 258
CRW_01271 - 0.32 0.29 0.34 111 827216 225 31 183 11 270
CRW_01344 - 0.37 0.29 0.47 105 791689 125 22 95 8 261
PDB_00409 - 0.34 0.38 0.31 94 688247 282 63 147 72 151
PDB_00805 - 0.64 0.59 0.70 177 467775 99 11 65 23 125
PDB_01261 - 0.59 0.43 0.79 146 467843 43 2 37 4 190

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Performance of RNAwolf - scored lower in this pairwise comparison

1. Total counts & total scores for RNAwolf

Total Base Pair Counts
Total TP 4369
Total TN 45321852
Total FP 24745
Total FP CONTRA 3879
Total FP INCONS 14974
Total FP COMP 5892
Total FN 16244
Total Scores
MCC 0.199
Average MCC ± 95% Confidence Intervals 0.215 ± 0.027
Sensitivity 0.212
Positive Predictive Value 0.188
Nr of predictions 88

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00002 - 0.28 0.29 0.27 76 408775 248 40 169 39 188
CRW_00417 - 0.16 0.16 0.15 43 458123 262 39 198 25 219
CRW_00418 - 0.14 0.15 0.14 38 441051 257 48 193 16 222
CRW_00419 - 0.13 0.14 0.12 36 463875 271 46 209 16 229
CRW_00421 - 0.17 0.18 0.16 48 462897 276 52 206 18 218
CRW_00422 - 0.15 0.16 0.14 41 455242 274 39 213 22 222
CRW_00424 - 0.20 0.21 0.19 75 789009 339 43 269 27 288
CRW_00426 - 0.22 0.23 0.22 60 457173 236 41 172 23 205
CRW_00427 - 0.26 0.26 0.26 69 454312 242 35 165 42 192
CRW_00428 - 0.17 0.18 0.16 48 465797 277 52 198 27 212
CRW_00430 - 0.10 0.11 0.10 29 456197 279 45 219 15 237
CRW_00433 - 0.20 0.20 0.19 53 467752 243 36 187 20 210
CRW_00434 - 0.14 0.15 0.14 39 457167 272 43 197 32 224
CRW_00435 - 0.17 0.17 0.17 45 451453 253 34 193 26 220
CRW_00437 - 0.26 0.27 0.26 69 456226 230 32 163 35 191
CRW_00438 - 0.16 0.16 0.15 44 454297 253 44 196 13 224
CRW_00441 - 0.14 0.15 0.14 38 454303 253 49 191 13 224
CRW_00442 - 0.15 0.15 0.14 39 453356 254 41 192 21 222
CRW_00443 - 0.20 0.20 0.20 52 456224 251 42 172 37 208
CRW_00444 - 0.23 0.24 0.23 62 459095 240 39 165 36 201
CRW_00445 - 0.23 0.25 0.22 65 458114 258 46 178 34 200
CRW_00446 - 0.11 0.11 0.10 30 468710 276 47 209 20 235
CRW_00447 - 0.14 0.15 0.13 38 452387 274 38 213 23 222
CRW_00448 - 0.08 0.08 0.08 22 457185 260 47 192 21 239
CRW_00449 - 0.09 0.10 0.09 25 444821 265 45 205 15 235
CRW_00450 - 0.17 0.18 0.16 46 458120 263 37 200 26 216
CRW_00451 - 0.18 0.19 0.18 51 457155 266 47 193 26 213
CRW_00452 - 0.14 0.15 0.13 39 453337 275 42 210 23 223
CRW_00453 - 0.25 0.25 0.25 64 452419 227 33 160 34 197
CRW_00456 - 0.19 0.19 0.19 50 470672 235 38 175 22 215
CRW_00457 - 0.27 0.28 0.27 75 467746 248 26 181 41 189
CRW_00458 - 0.27 0.27 0.27 71 464866 208 41 152 15 193
CRW_00459 - 0.22 0.23 0.22 60 461968 248 35 178 35 203
CRW_00462 - 0.19 0.20 0.18 51 458126 254 29 197 28 210
CRW_00463 - 0.21 0.22 0.20 56 445761 243 47 176 20 198
CRW_00464 - 0.17 0.17 0.17 44 461979 238 40 178 20 220
CRW_00530 - 0.24 0.27 0.22 72 534761 278 73 189 16 196
CRW_00532 - 0.18 0.20 0.16 54 579094 303 69 209 25 211
CRW_00533 - 0.28 0.31 0.26 67 453372 266 43 146 77 152
CRW_00538 - 0.21 0.24 0.18 72 811777 358 86 240 32 228
CRW_00604 - 0.81 0.81 0.80 66 411696 242 2 14 226 15
CRW_00606 - 0.72 0.73 0.72 67 559060 311 5 21 285 25
CRW_00607 - 0.45 0.45 0.44 35 536050 325 12 33 280 42
CRW_00615 - 0.44 0.55 0.36 45 553753 334 38 42 254 37
CRW_00617 - 0.07 0.09 0.05 6 426305 316 43 72 201 58
CRW_00678 - 0.16 0.18 0.14 22 666279 384 32 102 250 99
CRW_00680 - 0.25 0.28 0.23 34 516487 293 22 93 178 88
CRW_00683 - 0.10 0.13 0.09 17 460126 313 48 129 136 118
CRW_00684 - 0.10 0.13 0.09 17 611976 357 48 130 179 118
CRW_00702 - 0.30 0.35 0.25 26 357333 263 32 44 187 49
CRW_00704 - 0.33 0.36 0.31 34 386650 255 25 51 179 60
CRW_00706 - 0.43 0.46 0.40 27 695542 380 10 31 339 32
CRW_00713 - 0.38 0.41 0.35 41 731327 351 24 53 274 60
CRW_00730 - 0.42 0.46 0.39 74 338884 207 22 96 89 87
CRW_00734 - 0.19 0.25 0.14 28 536966 318 85 87 146 82
CRW_00735 - 0.18 0.23 0.13 28 677820 354 81 101 172 93
CRW_00740 - 0.03 0.04 0.02 5 489307 321 131 112 78 108
CRW_00746 - 0.22 0.24 0.19 53 550453 297 42 177 78 166
CRW_00750 - 0.12 0.12 0.12 19 709674 362 28 115 219 141
CRW_00751 - 0.51 0.54 0.48 96 489353 226 22 84 120 82
CRW_00753 - 0.09 0.10 0.08 18 489326 306 44 167 95 160
CRW_00757 - 0.12 0.15 0.10 19 415231 297 55 111 131 107
CRW_00765 - 0.13 0.14 0.12 37 452376 272 55 208 9 220
CRW_00766 - 0.14 0.15 0.13 35 440129 259 41 186 32 205
CRW_00768 - 0.30 0.32 0.29 83 471617 239 48 158 33 176
CRW_00769 - 0.21 0.23 0.20 58 451429 261 51 187 23 194
CRW_00773 - 0.32 0.33 0.31 85 451453 218 45 142 31 174
CRW_00774 - 0.15 0.16 0.14 42 488276 276 32 216 28 221
CRW_00777 - 0.09 0.10 0.08 31 719031 376 64 274 38 273
CRW_00780 - 0.19 0.20 0.18 50 475527 242 42 181 19 205
CRW_00783 - 0.13 0.14 0.12 35 453340 266 49 204 13 224
CRW_00784 - 0.17 0.18 0.16 48 456191 277 37 214 26 214
CRW_00785 - 0.21 0.22 0.21 55 452412 242 43 166 33 198
CRW_00787 - 0.18 0.19 0.18 59 646617 305 35 242 28 247
CRW_00794 - 0.13 0.15 0.12 36 434484 283 53 205 25 210
CRW_00796 - 0.05 0.06 0.05 14 384732 272 52 205 15 221
CRW_00797 - 0.13 0.14 0.12 47 692868 356 57 281 18 295
CRW_00801 - 0.18 0.19 0.17 48 438233 249 59 176 14 201
CRW_00802 - 0.12 0.13 0.11 33 460031 275 47 209 19 220
CRW_00813 - 0.11 0.15 0.08 20 530728 326 95 122 109 113
CRW_01186 - 0.19 0.19 0.18 75 836163 348 55 278 15 311
CRW_01250 - 0.22 0.22 0.22 85 781486 328 41 263 24 293
CRW_01266 - 0.19 0.20 0.18 76 818139 366 54 291 21 305
CRW_01271 - 0.17 0.17 0.17 65 827149 364 36 291 37 316
CRW_01344 - 0.16 0.16 0.16 59 791531 333 54 267 12 307
PDB_00409 - 0.29 0.34 0.24 84 688207 347 81 179 87 161
PDB_00805 - 0.34 0.36 0.33 108 467696 243 40 184 19 194
PDB_01261 - 0.52 0.50 0.54 168 467715 157 13 132 12 168

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

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