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 0.630 > 0.500
Average MCC ± 95% Confidence Intervals 0.675 ± 0.057 > 0.585 ± 0.066
Sensitivity 0.561 > 0.432
Positive Predictive Value 0.712 > 0.584
Total TP 1607 > 1237
Total TN 439721 < 439859
Total FP 770 < 961
Total FP CONTRA 74 < 108
Total FP INCONS 575 < 773
Total FP COMP 121 > 80
Total FN 1255 < 1625
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 1607
Total TN 439721
Total FP 770
Total FP CONTRA 74
Total FP INCONS 575
Total FP COMP 121
Total FN 1255
Total Scores
MCC 0.630
Average MCC ± 95% Confidence Intervals 0.675 ± 0.057
Sensitivity 0.561
Positive Predictive Value 0.712
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 9 222 0 0 0 0 0
2KE6_A 0.92 0.89 0.94 17 1110 2 0 1 1 2
2KPV_A - 0.96 0.92 1.00 12 549 0 0 0 0 1
2KRL_A - 0.76 0.60 0.96 24 5126 5 0 1 4 16
2KU0_A - -0.02 0.00 0.00 0 694 9 0 9 0 16
2KUR_A 0.90 0.86 0.95 18 1109 1 0 1 0 3
2KUU_A 0.87 0.81 0.94 17 1110 2 0 1 1 4
2KUV_A 0.88 0.82 0.95 18 1109 1 0 1 0 4
2KUW_A 0.90 0.86 0.95 18 1109 1 0 1 0 3
2KX8_A 0.94 0.89 1.00 16 845 0 0 0 0 2
2KXM_A - 0.83 0.70 1.00 7 344 0 0 0 0 3
2KZL_A - 0.86 0.74 1.00 14 1471 0 0 0 0 5
2L1F_B 0.98 0.96 1.00 24 2121 0 0 0 0 1
2L1F_A 0.98 0.96 1.00 23 2057 0 0 0 0 1
2L2K_A - 0.94 0.89 1.00 17 844 0 0 0 0 2
2L3C_B - 0.91 0.82 1.00 14 547 0 0 0 0 3
2L3E_A - 0.96 0.92 1.00 12 583 1 0 0 1 1
2L3J_B 0.94 0.88 1.00 30 2455 0 0 0 0 4
2L5Z_A - 0.86 0.75 1.00 9 316 0 0 0 0 3
2L94_A 0.97 0.95 1.00 19 971 0 0 0 0 1
2LA5_A - 0.39 0.26 0.63 5 622 3 1 2 0 14
2LBS_A - 1.00 1.00 1.00 14 482 0 0 0 0 0
2LC8_A -0.01 0.00 0.00 0 1525 15 2 13 0 20
2LDL_A - 0.90 0.82 1.00 9 342 1 0 0 1 2
2LDT_A - 0.85 0.73 1.00 11 454 0 0 0 0 4
2LHP_A - 0.97 0.94 1.00 15 651 0 0 0 0 1
2LI4_A - 0.93 0.88 1.00 14 482 0 0 0 0 2
2LJJ_A - 1.00 1.00 1.00 8 343 2 0 0 2 0
2LK3_A - 0.95 0.90 1.00 9 267 0 0 0 0 1
2LKR_A - 0.81 0.74 0.88 29 6072 6 0 4 2 10
2LWK_A - 0.88 0.85 0.92 11 484 1 0 1 0 2
2RRC_A - 0.70 0.50 1.00 5 226 0 0 0 0 5
2WRQ_Y 0.53 0.53 0.53 9 2833 13 5 3 5 8
2WW9_E - -0.01 0.00 0.00 0 556 5 0 5 0 14
2WW9_D - 0.14 0.12 0.19 3 1937 13 0 13 0 23
2WW9_F - 0.69 0.70 0.70 7 290 3 0 3 0 3
2WWQ_V 0.76 0.64 0.90 18 2906 3 0 2 1 10
2XKV_B 0.51 0.50 0.53 10 4541 24 0 9 15 10
2XQD_Y 0.88 0.78 1.00 21 2829 0 0 0 0 6
2XXA_G 0.25 0.24 0.27 10 5114 27 1 26 0 32
2Y8W_B - 1.00 1.00 1.00 6 184 1 0 0 1 0
2Y9C_V - 0.65 0.63 0.68 15 2256 8 1 6 1 9
2YIE_Z - -0.01 0.00 0.00 0 1525 15 3 12 0 12
2YIE_X - 0.36 0.33 0.40 4 1368 6 2 4 0 8
3A2K_C 0.42 0.39 0.46 11 2902 13 2 11 0 17
3ADB_C - 0.80 0.74 0.88 28 4154 4 0 4 0 10
3AKZ_H 0.84 0.75 0.95 21 2679 1 1 0 0 7
3AM1_B - 0.78 0.71 0.86 25 3211 4 0 4 0 10
3AMU_B 0.64 0.59 0.70 16 2980 9 0 7 2 11
3GX2_A 0.77 0.63 0.96 25 4345 2 0 1 1 15
3IAB_R - 0.92 0.86 1.00 12 1023 0 0 0 0 2
3IVN_B 0.78 0.61 1.00 19 2327 0 0 0 0 12
3IWN_A 0.74 0.67 0.81 22 4251 6 0 5 1 11
3IYQ_A 0.29 0.31 0.27 29 60617 84 19 61 4 65
3IZ4_A 0.54 0.46 0.64 61 70781 39 3 31 5 71
3IZF_C 0.71 0.61 0.83 33 6863 7 1 6 0 21
3J0L_g - -0.01 0.00 0.00 0 461 4 1 3 0 4
3J0L_8 - 0.93 0.88 1.00 7 183 0 0 0 0 1
3J0L_2 - 0.25 0.24 0.26 8 6185 25 2 21 2 25
3J0L_h - 0.81 0.65 1.00 28 6077 2 0 0 2 15
3J0L_1 - 0.76 0.63 0.92 12 1212 2 0 1 1 7
3J0L_7 - -0.01 0.00 0.00 0 1213 12 0 12 0 17
3J0L_a - 0.39 0.31 0.50 5 1118 5 2 3 0 11
3J16_L 0.29 0.23 0.37 7 2756 12 0 12 0 23
3J20_1 0.73 0.70 0.76 16 2905 5 0 5 0 7
3J20_0 0.44 0.40 0.50 12 2826 13 0 12 1 18
3J2C_O - 0.63 0.51 0.78 32 10255 10 0 9 1 31
3J2L_3 0.62 0.53 0.74 28 7837 12 0 10 2 25
3JYV_7 0.41 0.31 0.56 10 2832 8 0 8 0 22
3JYX_3 0.64 0.63 0.65 17 6302 19 1 8 10 10
3JYX_4 0.31 0.30 0.31 10 12214 34 4 18 12 23
3KTW_C - 0.54 0.47 0.65 20 4529 12 2 9 1 23
3LA5_A 0.78 0.62 1.00 21 2464 0 0 0 0 13
3NDB_M - 0.78 0.69 0.89 42 9133 6 0 5 1 19
3NKB_B - 0.59 0.54 0.67 14 1995 7 0 7 0 12
3NMU_E - -0.01 0.00 0.00 0 553 10 1 7 2 6
3NPB_A 0.71 0.61 0.82 28 6987 9 0 6 3 18
3O58_3 0.35 0.34 0.35 12 12369 35 2 20 13 23
3O58_2 0.75 0.76 0.74 29 7221 11 3 7 1 9
3OVB_D - 1.00 1.00 1.00 11 584 1 0 0 1 0
3OVS_D - 0.96 0.92 1.00 12 549 0 0 0 0 1
3P22_G - 0.96 0.92 1.00 11 730 0 0 0 0 1
3PDR_A 0.76 0.63 0.94 45 12832 5 0 3 2 27
3R4F_A - 0.96 0.92 1.00 23 2122 0 0 0 0 2
3R9X_C - 0.84 0.80 0.89 8 586 2 0 1 1 2
3RKF_A 0.76 0.59 1.00 20 2191 0 0 0 0 14
3SD1_A 0.58 0.48 0.71 20 3888 8 1 7 0 22
3SIU_F - 0.85 0.73 1.00 8 370 0 0 0 0 3
3SN2_B 1.00 1.00 1.00 12 394 0 0 0 0 0
3TRZ_Z - 0.91 0.83 1.00 5 205 1 0 0 1 1
3TS0_U - 1.00 1.00 1.00 6 247 1 0 0 1 0
3TS2_V - 1.00 1.00 1.00 5 271 0 0 0 0 0
3U4M_B - 0.45 0.35 0.59 13 3138 9 1 8 0 24
3UZL_B 0.77 0.62 0.96 23 3546 1 0 1 0 14
3VJR_D - 0.96 0.92 1.00 12 618 0 0 0 0 1
3W3S_B 0.88 0.78 1.00 31 4722 1 0 0 1 9
3ZEX_D 0.69 0.61 0.79 30 6983 8 1 7 0 19
3ZEX_E - 0.00 0.00 0.00 0 21893 54 2 50 2 77
4A1C_2 0.14 0.15 0.14 5 11746 41 4 26 11 28
4A1C_3 0.69 0.57 0.84 31 7103 6 0 6 0 23
4A4U_A - 1.00 1.00 1.00 9 222 0 0 0 0 0
4AOB_A 0.50 0.40 0.63 17 4344 11 2 8 1 25
4ATO_G - 0.38 0.30 0.50 3 522 3 0 3 0 7
4ENB_A 0.76 0.58 1.00 11 1264 0 0 0 0 8
4ENC_A 0.31 0.26 0.38 5 1313 8 1 7 0 14
4FRG_B 0.30 0.22 0.41 7 3469 10 1 9 0 25
4FRN_A 0.45 0.36 0.57 13 5128 10 2 8 0 23

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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 1237
Total TN 439859
Total FP 961
Total FP CONTRA 108
Total FP INCONS 773
Total FP COMP 80
Total FN 1625
Total Scores
MCC 0.500
Average MCC ± 95% Confidence Intervals 0.585 ± 0.066
Sensitivity 0.432
Positive Predictive Value 0.584
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 9 222 0 0 0 0 0
2KE6_A 0.97 0.95 1.00 18 1110 1 0 0 1 1
2KPV_A - 0.96 0.92 1.00 12 549 0 0 0 0 1
2KRL_A - 0.57 0.50 0.65 20 5120 11 5 6 0 20
2KU0_A - -0.02 0.00 0.00 0 692 11 0 11 0 16
2KUR_A 0.95 0.90 1.00 19 1109 0 0 0 0 2
2KUU_A 0.92 0.86 1.00 18 1110 1 0 0 1 3
2KUV_A 0.93 0.86 1.00 19 1109 0 0 0 0 3
2KUW_A 0.95 0.90 1.00 19 1109 0 0 0 0 2
2KX8_A 0.91 0.83 1.00 15 846 0 0 0 0 3
2KXM_A - 0.70 0.50 1.00 5 346 0 0 0 0 5
2KZL_A - 0.86 0.74 1.00 14 1471 0 0 0 0 5
2L1F_B 0.70 0.60 0.83 15 2127 3 0 3 0 10
2L1F_A 0.69 0.58 0.82 14 2063 3 0 3 0 10
2L2K_A - 0.89 0.79 1.00 15 846 0 0 0 0 4
2L3C_B - 0.91 0.82 1.00 14 547 0 0 0 0 3
2L3E_A - 0.96 0.92 1.00 12 583 1 0 0 1 1
2L3J_B 0.87 0.76 1.00 26 2459 0 0 0 0 8
2L5Z_A - 0.60 0.50 0.75 6 317 2 0 2 0 6
2L94_A 0.95 0.90 1.00 18 972 0 0 0 0 2
2LA5_A - -0.02 0.00 0.00 0 623 7 0 7 0 19
2LBS_A - 1.00 1.00 1.00 14 482 0 0 0 0 0
2LC8_A -0.01 0.00 0.00 0 1527 13 0 13 0 20
2LDL_A - 0.85 0.73 1.00 8 343 1 0 0 1 3
2LDT_A - 0.85 0.73 1.00 11 454 0 0 0 0 4
2LHP_A - 0.97 0.94 1.00 15 651 0 0 0 0 1
2LI4_A - 0.93 0.88 1.00 14 482 0 0 0 0 2
2LJJ_A - 1.00 1.00 1.00 8 343 2 0 0 2 0
2LK3_A - 0.89 0.80 1.00 8 268 0 0 0 0 2
2LKR_A - 0.27 0.23 0.32 9 6077 19 2 17 0 30
2LWK_A - 0.83 0.77 0.91 10 485 1 0 1 0 3
2RRC_A - 0.70 0.50 1.00 5 226 0 0 0 0 5
2WRQ_Y 0.53 0.53 0.53 9 2833 12 5 3 4 8
2WW9_E - -0.01 0.00 0.00 0 556 5 0 5 0 14
2WW9_D - 0.15 0.12 0.21 3 1939 11 1 10 0 23
2WW9_F - 0.59 0.60 0.60 6 290 4 0 4 0 4
2WWQ_V 0.64 0.50 0.82 14 2909 4 0 3 1 14
2XKV_B -0.01 0.00 0.00 0 4528 32 12 20 0 20
2XQD_Y 0.86 0.74 1.00 20 2830 0 0 0 0 7
2XXA_G -0.01 0.00 0.00 0 5120 31 2 29 0 42
2Y8W_B - 1.00 1.00 1.00 6 184 1 0 0 1 0
2Y9C_V - 0.61 0.54 0.68 13 2259 7 1 5 1 11
2YIE_Z - -0.01 0.00 0.00 0 1529 11 3 8 0 12
2YIE_X - 0.30 0.33 0.29 4 1364 10 2 8 0 8
3A2K_C 0.84 0.71 1.00 20 2906 0 0 0 0 8
3ADB_C - 0.67 0.53 0.87 20 4163 3 0 3 0 18
3AKZ_H 0.84 0.71 1.00 20 2681 0 0 0 0 8
3AM1_B - 0.78 0.71 0.86 25 3211 4 1 3 0 10
3AMU_B 0.67 0.59 0.76 16 2982 7 0 5 2 11
3GX2_A 0.51 0.40 0.67 16 4347 9 0 8 1 24
3IAB_R - 0.92 0.86 1.00 12 1023 0 0 0 0 2
3IVN_B 0.76 0.58 1.00 18 2328 0 0 0 0 13
3IWN_A 0.25 0.21 0.30 7 4255 16 1 15 0 26
3IYQ_A 0.33 0.31 0.35 29 60642 61 15 40 6 65
3IZ4_A 0.29 0.24 0.36 32 70787 62 8 49 5 100
3IZF_C 0.70 0.56 0.88 30 6869 4 0 4 0 24
3J0L_g - -0.01 0.00 0.00 0 461 4 1 3 0 4
3J0L_8 - 0.70 0.50 1.00 4 186 0 0 0 0 4
3J0L_2 - 0.35 0.33 0.37 11 6186 21 3 16 2 22
3J0L_h - 0.18 0.14 0.24 6 6080 19 1 18 0 37
3J0L_1 - 0.27 0.21 0.36 4 1214 7 1 6 0 15
3J0L_7 - -0.01 0.00 0.00 0 1212 13 0 13 0 17
3J0L_a - 0.39 0.31 0.50 5 1118 5 2 3 0 11
3J16_L 0.82 0.67 1.00 20 2755 0 0 0 0 10
3J20_1 0.71 0.70 0.73 16 2904 6 0 6 0 7
3J20_0 0.67 0.57 0.81 17 2829 5 1 3 1 13
3J2C_O - 0.30 0.24 0.39 15 10258 24 0 23 1 48
3J2L_3 0.56 0.45 0.71 24 7841 13 1 9 3 29
3JYV_7 -0.01 0.00 0.00 0 2831 19 0 19 0 32
3JYX_3 0.17 0.15 0.20 4 6308 18 4 12 2 23
3JYX_4 0.31 0.30 0.31 10 12214 32 3 19 10 23
3KTW_C - 0.38 0.30 0.50 13 4534 13 3 10 0 30
3LA5_A -0.01 0.00 0.00 0 2469 16 0 16 0 34
3NDB_M - 0.06 0.05 0.08 3 9144 33 1 32 0 58
3NKB_B - 0.59 0.54 0.67 14 1995 7 0 7 0 12
3NMU_E - 0.20 0.17 0.25 1 557 5 0 3 2 5
3NPB_A 0.57 0.46 0.72 21 6992 9 1 7 1 25
3O58_3 0.39 0.37 0.41 13 12371 28 7 12 9 22
3O58_2 0.45 0.42 0.48 16 7227 19 3 14 2 22
3OVB_D - 1.00 1.00 1.00 11 584 1 0 0 1 0
3OVS_D - 0.96 0.92 1.00 12 549 0 0 0 0 1
3P22_G - 0.96 0.92 1.00 11 730 0 0 0 0 1
3PDR_A 0.57 0.44 0.74 32 12837 13 0 11 2 40
3R4F_A - 0.94 0.88 1.00 22 2123 0 0 0 0 3
3R9X_C - 0.84 0.80 0.89 8 586 2 0 1 1 2
3RKF_A 0.75 0.65 0.88 22 2186 3 0 3 0 12
3SD1_A 0.11 0.10 0.15 4 3890 22 0 22 0 38
3SIU_F - 0.73 0.55 1.00 6 372 0 0 0 0 5
3SN2_B 0.96 0.92 1.00 11 395 0 0 0 0 1
3TRZ_Z - 0.91 0.83 1.00 5 205 1 0 0 1 1
3TS0_U - 1.00 1.00 1.00 6 247 1 0 0 1 0
3TS2_V - 1.00 1.00 1.00 5 271 0 0 0 0 0
3U4M_B - 0.38 0.32 0.46 12 3134 14 0 14 0 25
3UZL_B 0.16 0.14 0.20 5 3545 20 1 19 0 32
3VJR_D - 0.96 0.92 1.00 12 618 0 0 0 0 1
3W3S_B 0.76 0.70 0.82 28 4719 7 1 5 1 12
3ZEX_D 0.08 0.06 0.11 3 6994 24 0 24 0 46
3ZEX_E - 0.07 0.06 0.08 5 21886 54 5 49 0 72
4A1C_2 0.24 0.24 0.24 8 11748 37 3 22 12 25
4A1C_3 0.26 0.22 0.32 12 7103 25 2 23 0 42
4A4U_A - 1.00 1.00 1.00 9 222 0 0 0 0 0
4AOB_A 0.18 0.14 0.25 6 4347 19 1 17 1 36
4ATO_G - 0.56 0.60 0.55 6 517 5 1 4 0 4
4ENB_A 0.89 0.79 1.00 15 1260 0 0 0 0 4
4ENC_A 0.86 0.79 0.94 15 1310 1 1 0 0 4
4FRG_B 0.56 0.47 0.68 15 3464 7 1 6 0 17
4FRN_A 0.13 0.11 0.17 4 5128 19 2 17 0 32

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