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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric PknotsRG RNAwolf
MCC 0.328 > 0.199
Average MCC ± 95% Confidence Intervals 0.347 ± 0.030 > 0.215 ± 0.027
Sensitivity 0.327 > 0.212
Positive Predictive Value 0.329 > 0.188
Total TP 6738 > 4369
Total TN 45324594 > 45321852
Total FP 18380 < 24745
Total FP CONTRA 2661 < 3879
Total FP INCONS 11081 < 14974
Total FP COMP 4638 < 5892
Total FN 13875 < 16244
P-value 3.56938820447e-08

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Performance plots


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

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

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Performance of PknotsRG - scored higher in this pairwise comparison

1. Total counts & total scores for PknotsRG

Total Base Pair Counts
Total TP 6738
Total TN 45324594
Total FP 18380
Total FP CONTRA 2661
Total FP INCONS 11081
Total FP COMP 4638
Total FN 13875
Total Scores
MCC 0.328
Average MCC ± 95% Confidence Intervals 0.347 ± 0.030
Sensitivity 0.327
Positive Predictive Value 0.329
Nr of predictions 88

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00002 - 0.59 0.56 0.62 147 408824 142 7 82 53 117
CRW_00417 - 0.38 0.37 0.39 97 458154 163 22 130 11 165
CRW_00418 - 0.17 0.16 0.19 42 441104 195 25 159 11 218
CRW_00419 - 0.26 0.25 0.28 66 463932 175 16 152 7 199
CRW_00421 - 0.34 0.32 0.36 86 462964 166 22 131 13 180
CRW_00422 - 0.38 0.37 0.39 97 455287 169 22 129 18 166
CRW_00424 - 0.38 0.39 0.38 140 789031 253 23 202 28 223
CRW_00426 - 0.26 0.25 0.27 66 457200 190 24 156 10 199
CRW_00427 - 0.24 0.23 0.25 61 454339 196 32 149 15 200
CRW_00428 - 0.29 0.28 0.30 73 465855 179 27 140 12 187
CRW_00430 - 0.33 0.31 0.36 82 456260 154 27 121 6 184
CRW_00433 - 0.37 0.34 0.40 89 467805 139 16 118 5 174
CRW_00434 - 0.24 0.22 0.26 59 457218 179 11 158 10 204
CRW_00435 - 0.33 0.31 0.36 81 451499 155 16 129 10 184
CRW_00437 - 0.21 0.21 0.22 54 456243 200 25 168 7 206
CRW_00438 - 0.35 0.34 0.36 91 454325 175 25 140 10 177
CRW_00441 - 0.17 0.16 0.19 42 454358 185 31 150 4 220
CRW_00442 - 0.38 0.36 0.39 94 453389 153 25 120 8 167
CRW_00443 - 0.40 0.37 0.43 96 456268 147 23 103 21 164
CRW_00444 - 0.28 0.26 0.30 68 459131 169 33 129 7 195
CRW_00445 - 0.28 0.26 0.29 70 458165 178 24 144 10 195
CRW_00446 - 0.42 0.39 0.44 104 468762 140 16 114 10 161
CRW_00447 - 0.19 0.19 0.20 49 452433 207 33 161 13 211
CRW_00448 - 0.35 0.33 0.37 87 457211 166 26 122 18 174
CRW_00449 - 0.22 0.21 0.23 55 444853 191 24 164 3 205
CRW_00450 - 0.34 0.31 0.37 82 458184 155 13 124 18 180
CRW_00451 - 0.23 0.22 0.24 57 457204 199 24 161 14 207
CRW_00452 - 0.37 0.35 0.39 93 453390 155 24 121 10 169
CRW_00453 - 0.30 0.28 0.32 74 452448 164 23 131 10 187
CRW_00456 - 0.45 0.42 0.48 111 470705 135 19 100 16 154
CRW_00457 - 0.32 0.31 0.34 81 467792 167 22 133 12 183
CRW_00458 - 0.35 0.34 0.37 90 464887 164 30 123 11 174
CRW_00459 - 0.29 0.27 0.31 71 462012 175 27 131 17 192
CRW_00462 - 0.38 0.36 0.41 93 458178 151 18 114 19 168
CRW_00463 - 0.36 0.35 0.37 90 445799 160 21 130 9 164
CRW_00464 - 0.39 0.36 0.42 95 462015 141 15 116 10 169
CRW_00530 - 0.35 0.37 0.33 99 534795 217 51 150 16 169
CRW_00532 - 0.19 0.20 0.17 54 579117 268 65 190 13 211
CRW_00533 - 0.19 0.22 0.16 49 453325 263 90 164 9 170
CRW_00538 - 0.20 0.21 0.19 62 811841 294 70 202 22 238
CRW_00604 - 0.52 0.57 0.48 46 411682 216 14 36 166 35
CRW_00606 - 0.67 0.65 0.69 60 559066 262 4 23 235 32
CRW_00607 - 0.54 0.55 0.53 42 536051 276 8 29 239 35
CRW_00615 - 0.50 0.57 0.44 47 553770 285 24 37 224 35
CRW_00617 - 0.69 0.69 0.69 44 426362 237 1 19 217 20
CRW_00678 - 0.42 0.48 0.37 58 666280 305 27 70 208 63
CRW_00680 - 0.30 0.34 0.27 41 516483 253 27 85 141 81
CRW_00683 - 0.44 0.47 0.41 63 460166 242 29 62 151 72
CRW_00684 - 0.36 0.39 0.33 53 612010 296 36 72 188 82
CRW_00702 - 0.66 0.72 0.61 54 357346 213 10 25 178 21
CRW_00704 - 0.81 0.80 0.82 75 386669 195 4 12 179 19
CRW_00706 - 0.46 0.51 0.42 30 695538 341 7 35 299 29
CRW_00713 - 0.65 0.65 0.65 66 731343 308 11 25 272 35
CRW_00730 - 0.46 0.51 0.42 82 338879 185 33 82 70 79
CRW_00734 - 0.21 0.29 0.15 32 536958 260 99 77 84 78
CRW_00735 - 0.26 0.34 0.20 41 677825 298 90 74 134 80
CRW_00740 - 0.00 0.00 0.00 0 489333 296 100 122 74 113
CRW_00746 - 0.42 0.43 0.40 95 550488 210 34 108 68 124
CRW_00750 - 0.25 0.29 0.21 46 709621 315 51 118 146 114
CRW_00751 - 0.57 0.62 0.53 110 489348 185 36 61 88 68
CRW_00753 - 0.15 0.16 0.13 29 489339 268 49 138 81 149
CRW_00757 - 0.08 0.10 0.07 13 415225 258 65 113 80 113
CRW_00765 - 0.24 0.24 0.24 62 452416 208 35 163 10 195
CRW_00766 - 0.22 0.22 0.23 52 440169 187 23 147 17 188
CRW_00768 - 0.60 0.58 0.62 150 471663 116 14 79 23 109
CRW_00769 - 0.40 0.37 0.42 94 451502 146 20 109 17 158
CRW_00773 - 0.34 0.34 0.33 88 451460 186 30 147 9 171
CRW_00774 - 0.35 0.33 0.38 87 488335 169 17 127 25 176
CRW_00777 - 0.30 0.31 0.29 93 719076 260 47 184 29 211
CRW_00780 - 0.32 0.31 0.34 79 475565 169 23 133 13 176
CRW_00783 - 0.31 0.31 0.31 80 453374 183 18 156 9 179
CRW_00784 - 0.34 0.33 0.36 86 456250 171 32 122 17 176
CRW_00785 - 0.35 0.33 0.36 84 452443 161 27 122 12 169
CRW_00787 - 0.26 0.26 0.26 81 646638 256 41 193 22 225
CRW_00794 - 0.24 0.24 0.24 58 434539 200 18 163 19 188
CRW_00796 - 0.25 0.24 0.26 57 384786 182 29 131 22 178
CRW_00797 - 0.22 0.23 0.22 79 692890 299 41 243 15 263
CRW_00801 - 0.45 0.45 0.45 111 438269 150 33 103 14 138
CRW_00802 - 0.31 0.30 0.31 76 460076 184 36 132 16 177
CRW_00813 - 0.20 0.23 0.17 31 530781 292 52 101 139 102
CRW_01186 - 0.27 0.27 0.27 104 836186 293 35 246 12 282
CRW_01250 - 0.24 0.24 0.24 89 781505 291 39 242 10 289
CRW_01266 - 0.27 0.28 0.27 105 818167 301 42 246 13 276
CRW_01271 - 0.30 0.30 0.30 116 827149 289 35 241 13 265
CRW_01344 - 0.33 0.33 0.34 120 791554 252 45 192 15 246
PDB_00409 - 0.28 0.32 0.24 79 688221 321 66 185 70 166
PDB_00805 - 0.69 0.67 0.71 201 467744 108 13 70 25 101
PDB_01261 - 0.50 0.45 0.55 152 467752 128 4 120 4 184

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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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