CompaRNA - on-line benchmarks of RNA structure prediction methods
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Table of contents:

  1. Overview

  2. Performance Plots

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

  4. Performance of Vsfold5 - scored lower in this pairwise comparison

  5. Compile and download dataset for MaxExpect & Vsfold5 [.zip] - may take several seconds...


Overview

Metric MaxExpect Vsfold5
MCC 0.731 > 0.578
Average MCC ± 95% Confidence Intervals 0.753 ± 0.061 > 0.645 ± 0.070
Sensitivity 0.744 > 0.579
Positive Predictive Value 0.725 > 0.588
Total TP 1537 > 1197
Total TN 165133 < 165218
Total FP 840 < 1001
Total FP CONTRA 173 < 239
Total FP INCONS 411 < 600
Total FP COMP 256 > 162
Total FN 529 < 869
P-value 3.56938820447e-08

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Performance plots


  1. Comparison of performance of MaxExpect and Vsfold5. 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 MaxExpect and Vsfold5).

  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 MaxExpect and Vsfold5).

  3. Comparison of average Matthews Correlation Coefficients (MCCs) for MaxExpect and Vsfold5. 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 MaxExpect and Vsfold5).

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Performance of MaxExpect - scored higher in this pairwise comparison

1. Total counts & total scores for MaxExpect

Total Base Pair Counts
Total TP 1537
Total TN 165133
Total FP 840
Total FP CONTRA 173
Total FP INCONS 411
Total FP COMP 256
Total FN 529
Total Scores
MCC 0.731
Average MCC ± 95% Confidence Intervals 0.753 ± 0.061
Sensitivity 0.744
Positive Predictive Value 0.725
Nr of predictions 107

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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
2KD8_A - 1.00 1.00 1.00 9 99 0 0 0 0 0
2KE6_A 0.94 0.94 0.94 17 449 2 0 1 1 1
2KPV_A - 0.96 0.92 1.00 12 201 0 0 0 0 1
2KRL_A - 0.91 0.87 0.95 20 2003 9 1 0 8 3
2KU0_A - -0.04 0.00 0.00 0 283 9 1 8 0 12
2KUR_A 0.95 0.95 0.95 18 448 1 0 1 0 1
2KUU_A 0.94 0.94 0.94 17 429 2 0 1 1 1
2KUV_A 0.94 0.95 0.95 18 420 1 0 1 0 1
2KUW_A 0.94 0.94 0.94 17 452 2 0 1 1 1
2KX8_A 1.00 1.00 1.00 16 355 0 0 0 0 0
2KXM_A - 0.93 0.88 1.00 7 142 0 0 0 0 1
2KZL_A - 1.00 1.00 1.00 13 507 1 0 0 1 0
2L1F_B 1.00 1.00 1.00 24 767 0 0 0 0 0
2L1F_A 1.00 1.00 1.00 23 740 0 0 0 0 0
2L2K_A - 1.00 1.00 1.00 17 332 0 0 0 0 0
2L3C_B - 1.00 1.00 1.00 14 225 0 0 0 0 0
2L3E_A - 1.00 1.00 1.00 12 228 1 0 0 1 0
2L3J_B 1.00 1.00 1.00 30 955 0 0 0 0 0
2L5Z_A - 1.00 1.00 1.00 9 102 0 0 0 0 0
2L94_A 1.00 1.00 1.00 18 339 1 0 0 1 0
2LA5_A - 0.77 0.71 0.83 5 269 3 0 1 2 2
2LBS_A - 1.00 1.00 1.00 14 193 0 0 0 0 0
2LC8_A -0.03 0.00 0.00 0 513 15 3 12 0 18
2LDL_A - 1.00 1.00 1.00 9 131 1 0 0 1 0
2LDT_A - 1.00 1.00 1.00 11 151 0 0 0 0 0
2LHP_A - 1.00 1.00 1.00 15 246 0 0 0 0 0
2LI4_A - 1.00 1.00 1.00 14 175 0 0 0 0 0
2LJJ_A - 1.00 1.00 1.00 7 123 3 0 0 3 0
2LK3_A - 1.00 1.00 1.00 9 91 0 0 0 0 0
2LKR_A - 0.84 0.83 0.86 24 2412 11 0 4 7 5
2LWK_A - 1.00 1.00 1.00 11 196 1 0 0 1 0
2RRC_A - 0.83 0.71 1.00 5 70 0 0 0 0 2
2WRQ_Y 0.94 0.89 1.00 8 1144 14 0 0 14 1
2WW9_E - -0.03 0.00 0.00 0 168 5 0 4 1 5
2WW9_D - 0.08 0.10 0.08 1 729 15 2 9 4 9
2WW9_F - 0.64 0.75 0.60 6 102 4 1 3 0 2
2WWQ_V 0.97 0.95 1.00 18 1186 3 0 0 3 1
2XKV_B 0.64 0.73 0.57 8 1821 26 0 6 20 3
2XQD_Y 0.98 0.95 1.00 20 1109 1 0 0 1 1
2XXA_G 0.24 0.26 0.25 9 2009 28 1 26 1 26
2Y8W_B - 1.00 1.00 1.00 6 82 1 0 0 1 0
2Y9C_V - 0.79 0.83 0.75 15 886 8 0 5 3 3
2YIE_Z - -0.02 0.00 0.00 0 587 15 6 9 0 8
2YIE_X - 0.53 0.57 0.50 4 536 6 1 3 2 3
3A2K_C 0.47 0.50 0.46 11 1084 13 3 10 0 11
3ADB_C - 0.86 0.85 0.88 28 1787 4 0 4 0 5
3AKZ_H 1.00 1.00 1.00 20 1107 2 0 0 2 0
3AM1_B - 0.86 0.86 0.86 25 1437 4 0 4 0 4
3AMU_B 0.73 0.79 0.68 15 1135 10 0 7 3 4
3GX2_A 0.93 0.89 0.96 25 1423 2 1 0 1 3
3IAB_R - 1.00 1.00 1.00 12 373 0 0 0 0 0
3IVN_B 0.91 0.83 1.00 19 884 0 0 0 0 4
3IWN_A 0.80 0.79 0.81 22 1445 6 1 4 1 6
3IYQ_A 0.24 0.33 0.17 17 22342 96 41 40 15 34
3IZ4_A 0.61 0.61 0.62 58 25442 42 14 22 6 37
3IZF_C 0.89 0.91 0.86 32 2603 8 0 5 3 3
3J0L_g - -0.01 0.00 0.00 0 174 4 0 2 2 2
3J0L_8 - 1.00 1.00 1.00 7 69 0 0 0 0 0
3J0L_2 - 0.30 0.31 0.31 8 2224 25 2 16 7 18
3J0L_h - 0.93 0.88 1.00 28 2112 2 0 0 2 4
3J0L_1 - 0.83 0.77 0.91 10 473 4 0 1 3 3
3J0L_7 - -0.02 0.00 0.00 0 507 12 3 9 0 10
3J0L_a - 0.39 0.36 0.44 4 402 6 4 1 1 7
3J16_L 0.34 0.33 0.37 7 1140 12 0 12 0 14
3J20_1 0.75 0.75 0.75 15 1092 6 0 5 1 5
3J20_0 0.53 0.57 0.50 12 1195 13 2 10 1 9
3J2C_O - 0.74 0.71 0.78 29 3950 13 0 8 5 12
3J2L_3 0.80 0.82 0.78 28 2984 12 1 7 4 6
3JYV_7 0.48 0.45 0.53 9 1094 9 3 5 1 11
3JYX_3 0.77 0.80 0.75 12 2362 24 0 4 20 3
3JYX_4 0.55 0.83 0.37 10 4729 34 14 3 17 2
3KTW_C - 0.72 0.72 0.72 18 1755 14 2 5 7 7
3LA5_A 0.91 0.84 1.00 21 933 0 0 0 0 4
3NDB_M - 0.94 0.93 0.95 41 3671 7 0 2 5 3
3NKB_B - 0.69 0.74 0.67 14 714 7 0 7 0 5
3NMU_E - -0.02 0.00 0.00 0 208 10 5 3 2 3
3NPB_A 0.77 0.73 0.82 27 2245 10 0 6 4 10
3O58_3 0.40 0.50 0.33 11 4731 36 8 14 14 11
3O58_2 0.91 0.94 0.88 29 2721 11 0 4 7 2
3OVB_D - 1.00 1.00 1.00 11 215 1 0 0 1 0
3OVS_D - 1.00 1.00 1.00 12 204 0 0 0 0 0
3P22_G - 1.00 1.00 1.00 11 301 0 0 0 0 0
3PDR_A 0.92 0.90 0.94 45 4792 5 1 2 2 5
3R4F_A - 1.00 1.00 1.00 22 884 1 0 0 1 0
3R9X_C - 1.00 1.00 1.00 8 221 2 0 0 2 0
3RKF_A 0.91 0.83 1.00 20 846 0 0 0 0 4
3SD1_A 0.70 0.69 0.71 20 1505 8 3 5 0 9
3SIU_F - 1.00 1.00 1.00 8 137 0 0 0 0 0
3SN2_B 1.00 1.00 1.00 12 142 0 0 0 0 0
3TRZ_Z - 1.00 1.00 1.00 5 87 1 0 0 1 0
3TS0_U - 1.00 1.00 1.00 6 112 1 0 0 1 0
3TS2_V - 1.00 1.00 1.00 5 103 0 0 0 0 0
3U4M_B - 0.58 0.59 0.59 13 1254 9 2 7 0 9
3UZL_B 1.00 1.00 1.00 16 1277 8 0 0 8 0
3VJR_D - 1.00 1.00 1.00 12 239 0 0 0 0 0
3W3S_B 0.97 0.94 1.00 31 1958 1 0 0 1 2
3ZEX_D 0.82 0.77 0.87 27 2765 11 0 4 7 8
3ZEX_E - -0.01 0.00 0.00 0 8252 54 21 31 2 34
4A1C_2 0.19 0.25 0.16 5 4484 41 10 17 14 15
4A1C_3 0.83 0.81 0.86 30 2728 7 0 5 2 7
4A4U_A - 1.00 1.00 1.00 9 96 0 0 0 0 0
4AOB_A 0.60 0.59 0.63 17 1410 11 4 6 1 12
4ATO_G - 0.45 0.43 0.50 3 214 3 3 0 0 4
4ENB_A 0.85 0.73 1.00 11 461 0 0 0 0 4
4ENC_A 0.36 0.33 0.42 5 484 8 0 7 1 10
4FRG_B 0.29 0.25 0.35 6 1185 11 4 7 0 18
4FRN_A 0.51 0.46 0.57 13 1825 10 5 5 0 15

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Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

Total Base Pair Counts
Total TP 1197
Total TN 165218
Total FP 1001
Total FP CONTRA 239
Total FP INCONS 600
Total FP COMP 162
Total FN 869
Total Scores
MCC 0.578
Average MCC ± 95% Confidence Intervals 0.645 ± 0.070
Sensitivity 0.579
Positive Predictive Value 0.588
Nr of predictions 107

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2. Individual counts for Vsfold5 [ download as .csv ]

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
2KD8_A - 1.00 1.00 1.00 9 99 0 0 0 0 0
2KE6_A 1.00 1.00 1.00 18 449 1 0 0 1 0
2KPV_A - 0.96 0.92 1.00 12 201 0 0 0 0 1
2KRL_A - 0.71 0.78 0.64 18 1996 13 8 2 3 5
2KU0_A - -0.04 0.00 0.00 0 281 11 0 11 0 12
2KUR_A 1.00 1.00 1.00 19 448 0 0 0 0 0
2KUU_A 1.00 1.00 1.00 18 429 1 0 0 1 0
2KUV_A 1.00 1.00 1.00 19 420 0 0 0 0 0
2KUW_A 1.00 1.00 1.00 18 452 1 0 0 1 0
2KX8_A 0.97 0.94 1.00 15 356 0 0 0 0 1
2KXM_A - 0.78 0.63 1.00 5 144 0 0 0 0 3
2KZL_A - 1.00 1.00 1.00 13 507 1 0 0 1 0
2L1F_B 0.71 0.63 0.83 15 773 3 0 3 0 9
2L1F_A 0.70 0.61 0.82 14 746 3 0 3 0 9
2L2K_A - 0.94 0.88 1.00 15 334 0 0 0 0 2
2L3C_B - 1.00 1.00 1.00 14 225 0 0 0 0 0
2L3E_A - 1.00 1.00 1.00 12 228 1 0 0 1 0
2L3J_B 0.93 0.87 1.00 26 959 0 0 0 0 4
2L5Z_A - 0.68 0.67 0.75 6 103 2 0 2 0 3
2L94_A 0.97 0.94 1.00 17 340 1 0 0 1 1
2LA5_A - -0.03 0.00 0.00 0 268 7 0 7 0 7
2LBS_A - 1.00 1.00 1.00 14 193 0 0 0 0 0
2LC8_A -0.03 0.00 0.00 0 515 13 0 13 0 18
2LDL_A - 0.94 0.89 1.00 8 132 1 0 0 1 1
2LDT_A - 1.00 1.00 1.00 11 151 0 0 0 0 0
2LHP_A - 1.00 1.00 1.00 15 246 0 0 0 0 0
2LI4_A - 1.00 1.00 1.00 14 175 0 0 0 0 0
2LJJ_A - 1.00 1.00 1.00 7 123 3 0 0 3 0
2LK3_A - 0.94 0.89 1.00 8 92 0 0 0 0 1
2LKR_A - 0.31 0.31 0.32 9 2412 19 5 14 0 20
2LWK_A - 0.95 0.91 1.00 10 197 1 0 0 1 1
2RRC_A - 0.83 0.71 1.00 5 70 0 0 0 0 2
2WRQ_Y 0.94 0.89 1.00 8 1144 13 0 0 13 1
2WW9_E - -0.03 0.00 0.00 0 168 5 0 4 1 5
2WW9_D - 0.08 0.10 0.09 1 730 13 3 7 3 9
2WW9_F - 0.68 0.75 0.67 6 103 4 1 2 1 2
2WWQ_V 0.78 0.74 0.82 14 1187 4 1 2 1 5
2XKV_B -0.01 0.00 0.00 0 1803 32 17 15 0 11
2XQD_Y 0.95 0.90 1.00 19 1110 1 0 0 1 2
2XXA_G -0.02 0.00 0.00 0 2014 31 2 29 0 35
2Y8W_B - 1.00 1.00 1.00 6 82 1 0 0 1 0
2Y9C_V - 0.74 0.72 0.76 13 889 7 0 4 3 5
2YIE_Z - -0.02 0.00 0.00 0 591 11 5 6 0 8
2YIE_X - 0.43 0.57 0.33 4 532 10 2 6 2 3
3A2K_C 0.95 0.91 1.00 20 1088 0 0 0 0 2
3ADB_C - 0.72 0.61 0.87 20 1796 3 0 3 0 13
3AKZ_H 0.97 0.95 1.00 19 1108 1 0 0 1 1
3AM1_B - 0.86 0.86 0.86 25 1437 4 3 1 0 4
3AMU_B 0.77 0.79 0.75 15 1137 8 0 5 3 4
3GX2_A 0.61 0.57 0.67 16 1425 9 0 8 1 12
3IAB_R - 1.00 1.00 1.00 12 373 0 0 0 0 0
3IVN_B 0.88 0.78 1.00 18 885 0 0 0 0 5
3IWN_A 0.26 0.25 0.30 7 1449 16 2 14 0 21
3IYQ_A 0.30 0.37 0.24 19 22361 71 36 24 11 32
3IZ4_A 0.31 0.31 0.33 29 25448 65 14 45 6 66
3IZF_C 0.85 0.83 0.88 29 2607 5 0 4 1 6
3J0L_g - -0.01 0.00 0.00 0 174 4 0 2 2 2
3J0L_8 - 0.74 0.57 1.00 4 72 0 0 0 0 3
3J0L_2 - 0.42 0.42 0.44 11 2225 21 1 13 7 15
3J0L_h - 0.20 0.19 0.24 6 2115 19 3 16 0 26
3J0L_1 - 0.25 0.23 0.30 3 474 8 3 4 1 10
3J0L_7 - -0.02 0.00 0.00 0 506 13 3 10 0 10
3J0L_a - 0.39 0.36 0.44 4 402 6 4 1 1 7
3J16_L 0.98 0.95 1.00 20 1139 0 0 0 0 1
3J20_1 0.75 0.75 0.75 15 1092 7 0 5 2 5
3J20_0 0.76 0.76 0.76 16 1198 6 3 2 1 5
3J2C_O - 0.33 0.32 0.36 13 3951 26 3 20 3 28
3J2L_3 0.70 0.71 0.71 24 2986 13 3 7 3 10
3JYV_7 -0.02 0.00 0.00 0 1092 19 4 15 0 20
3JYX_3 0.12 0.13 0.11 2 2360 20 6 10 4 13
3JYX_4 0.63 0.83 0.48 10 4735 32 9 2 21 2
3KTW_C - 0.46 0.44 0.50 11 1758 15 2 9 4 14
3LA5_A -0.02 0.00 0.00 0 938 16 0 16 0 25
3NDB_M - 0.07 0.07 0.08 3 3678 33 2 31 0 41
3NKB_B - 0.69 0.74 0.67 14 714 7 0 7 0 5
3NMU_E - 0.28 0.33 0.25 1 212 5 2 1 2 2
3NPB_A 0.62 0.54 0.71 20 2250 10 1 7 2 17
3O58_3 0.51 0.59 0.45 13 4735 28 11 5 12 9
3O58_2 0.50 0.52 0.50 16 2722 19 3 13 3 15
3OVB_D - 1.00 1.00 1.00 11 215 1 0 0 1 0
3OVS_D - 1.00 1.00 1.00 12 204 0 0 0 0 0
3P22_G - 1.00 1.00 1.00 11 301 0 0 0 0 0
3PDR_A 0.69 0.64 0.74 32 4797 13 3 8 2 18
3R4F_A - 0.98 0.95 1.00 21 885 1 0 0 1 1
3R9X_C - 1.00 1.00 1.00 8 221 2 0 0 2 0
3RKF_A 0.90 0.92 0.88 22 841 3 3 0 0 2
3SD1_A 0.13 0.14 0.15 4 1507 22 5 17 0 25
3SIU_F - 0.86 0.75 1.00 6 139 0 0 0 0 2
3SN2_B 0.95 0.92 1.00 11 143 0 0 0 0 1
3TRZ_Z - 1.00 1.00 1.00 5 87 1 0 0 1 0
3TS0_U - 1.00 1.00 1.00 6 112 1 0 0 1 0
3TS2_V - 1.00 1.00 1.00 5 103 0 0 0 0 0
3U4M_B - 0.49 0.55 0.46 12 1250 14 3 11 0 10
3UZL_B 0.24 0.31 0.20 5 1268 20 9 11 0 11
3VJR_D - 1.00 1.00 1.00 12 239 0 0 0 0 0
3W3S_B 0.83 0.85 0.82 28 1955 7 2 4 1 5
3ZEX_D 0.09 0.09 0.12 3 2771 24 5 17 2 32
3ZEX_E - 0.11 0.15 0.09 5 8247 54 21 31 2 29
4A1C_2 0.33 0.40 0.28 8 4487 37 8 13 16 12
4A1C_3 0.29 0.30 0.31 11 2727 26 4 21 1 26
4A4U_A - 1.00 1.00 1.00 9 96 0 0 0 0 0
4AOB_A 0.21 0.21 0.25 6 1413 19 2 16 1 23
4ATO_G - 0.67 0.86 0.55 6 209 5 5 0 0 1
4ENB_A 1.00 1.00 1.00 15 457 0 0 0 0 0
4ENC_A 0.97 1.00 0.94 15 480 1 1 0 0 0
4FRG_B 0.60 0.58 0.64 14 1180 8 3 5 0 10
4FRN_A 0.15 0.14 0.17 4 1825 19 3 16 0 24

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