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

  1. Overview

  2. Performance Plots

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

  4. Performance of Carnac(seed) - scored lower in this pairwise comparison

  5. Compile and download dataset for Alterna & Carnac(seed) [.zip] - may take several seconds...


Overview

Metric Alterna Carnac(seed)
MCC 0.507 > 0.503
Average MCC ± 95% Confidence Intervals 0.526 ± 0.066 > 0.387 ± 0.084
Sensitivity 0.485 > 0.281
Positive Predictive Value 0.538 < 0.907
Total TP 686 > 398
Total TN 148958 < 149793
Total FP 725 > 87
Total FP CONTRA 78 > 4
Total FP INCONS 510 > 37
Total FP COMP 137 > 46
Total FN 729 < 1017
P-value 0.0617146490994

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Performance plots


  1. Comparison of performance of Alterna and Carnac(seed). 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 Alterna and Carnac(seed)).

  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 Alterna and Carnac(seed)).

  3. Comparison of average Matthews Correlation Coefficients (MCCs) for Alterna and Carnac(seed). 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 Alterna and Carnac(seed)).

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Performance of Alterna - scored higher in this pairwise comparison

1. Total counts & total scores for Alterna

Total Base Pair Counts
Total TP 686
Total TN 148958
Total FP 725
Total FP CONTRA 78
Total FP INCONS 510
Total FP COMP 137
Total FN 729
Total Scores
MCC 0.507
Average MCC ± 95% Confidence Intervals 0.526 ± 0.066
Sensitivity 0.485
Positive Predictive Value 0.538
Nr of predictions 89

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
PDB_00005 0.88 0.79 1.00 11 935 0 0 0 0 3
PDB_00012 1.00 1.00 1.00 7 399 3 0 0 3 0
PDB_00553 1.00 1.00 1.00 11 454 0 0 0 0 0
PDB_00716 -0.01 0.00 0.00 0 2680 21 3 18 0 23
PDB_00810 0.64 0.41 1.00 7 1074 1 0 0 1 10
PDB_01001 0.52 0.56 0.50 10 2125 10 3 7 0 8
PDB_01050 0.92 0.85 1.00 11 619 2 0 0 2 2
PDB_01051 0.55 0.54 0.58 7 891 6 1 4 1 6
PDB_01152 0.96 0.93 1.00 13 548 0 0 0 0 1
RFA_00389 0.97 0.93 1.00 14 1417 2 0 0 2 1
RFA_00390 1.00 1.00 1.00 15 1416 2 0 0 2 0
RFA_00391 0.80 0.80 0.80 12 1416 5 0 3 2 3
RFA_00409 0.97 0.93 1.00 14 1417 2 0 0 2 1
RFA_00416 0.93 0.93 0.93 14 1470 4 0 1 3 1
RFA_00433 1.00 1.00 1.00 15 1416 2 0 0 2 0
RFA_00434 1.00 1.00 1.00 15 1416 2 0 0 2 0
RFA_00436 1.00 1.00 1.00 15 1416 2 0 0 2 0
RFA_00440 0.97 0.93 1.00 14 1471 2 0 0 2 1
RFA_00442 1.00 1.00 1.00 15 1416 2 0 0 2 0
RFA_00446 0.97 0.93 1.00 14 1471 2 0 0 2 1
RFA_00449 0.97 0.93 1.00 14 1471 2 0 0 2 1
RFA_00587 1.00 1.00 1.00 15 4836 14 0 0 14 0
RFA_00632 0.24 0.25 0.23 7 4065 23 3 20 0 21
RFA_00636 0.50 0.46 0.54 13 3981 13 3 8 2 15
RFA_00642 0.16 0.17 0.17 3 2908 15 0 15 0 15
RFA_00643 0.24 0.22 0.27 4 2196 12 2 9 1 14
RFA_00644 -0.01 0.00 0.00 0 2682 19 3 16 0 18
RFA_00645 -0.01 0.00 0.00 0 2397 18 5 13 0 18
RFA_00649 0.31 0.33 0.30 6 2125 14 0 14 0 12
RFA_00651 0.35 0.33 0.38 6 2064 10 1 9 0 12
RFA_00653 0.34 0.33 0.35 6 2128 14 2 9 3 12
RFA_00654 -0.01 0.00 0.00 0 2399 16 2 14 0 18
RFA_00658 0.69 0.64 0.75 9 1116 5 0 3 2 5
RFA_00659 0.30 0.29 0.33 4 1116 10 0 8 2 10
RFA_00664 -0.01 0.00 0.00 0 980 10 0 10 0 14
RFA_00667 0.29 0.29 0.31 4 977 10 1 8 1 10
RFA_00668 0.60 0.43 0.86 6 983 1 0 1 0 8
RFA_00672 -0.01 0.00 0.00 0 895 9 0 8 1 13
RFA_00673 0.42 0.36 0.50 5 1118 6 0 5 1 9
RFA_00674 0.74 0.71 0.77 10 1115 4 0 3 1 4
RFA_00675 0.29 0.29 0.31 4 977 9 1 8 0 10
RFA_00677 0.59 0.57 0.62 8 977 7 0 5 2 6
RFA_00678 0.80 0.64 1.00 9 937 0 0 0 0 5
RFA_00680 0.74 0.71 0.77 10 1115 6 0 3 3 4
RFA_00684 0.77 0.71 0.83 10 978 4 0 2 2 4
RFA_00685 0.42 0.36 0.50 5 980 6 0 5 1 9
RFA_00703 0.69 0.64 0.75 9 4266 16 1 2 13 5
RFA_00704 0.36 0.36 0.38 5 977 9 0 8 1 9
RFA_00705 0.74 0.71 0.77 10 1022 4 0 3 1 4
RFA_00706 0.31 0.29 0.36 4 1024 7 0 7 0 10
RFA_00707 0.31 0.29 0.36 4 1024 7 0 7 0 10
RFA_00708 0.59 0.50 0.70 7 1025 4 0 3 1 7
RFA_00709 -0.01 0.00 0.00 0 982 9 0 8 1 14
RFA_00710 0.38 0.36 0.42 5 978 8 0 7 1 9
RFA_00711 -0.01 0.00 0.00 0 1026 9 0 9 0 14
RFA_00715 -0.01 0.00 0.00 0 933 13 0 13 0 14
RFA_00716 -0.01 0.00 0.00 0 936 10 0 10 0 14
RFA_00717 0.69 0.64 0.75 9 891 3 0 3 0 5
RFA_00730 0.69 0.67 0.73 8 892 5 1 2 2 4
RFA_00731 0.41 0.42 0.42 5 891 8 3 4 1 7
RFA_00733 0.43 0.42 0.45 5 892 7 1 5 1 7
RFA_00734 0.64 0.42 1.00 5 898 1 0 0 1 7
RFA_00736 0.41 0.42 0.42 5 891 8 3 4 1 7
RFA_00737 0.39 0.42 0.38 5 890 9 2 6 1 7
RFA_00745 0.43 0.42 0.45 5 935 7 1 5 1 7
RFA_00749 0.41 0.42 0.42 5 891 8 3 4 1 7
RFA_00758 0.57 0.33 1.00 4 899 1 0 0 1 8
RFA_00762 0.64 0.67 0.62 8 890 6 1 4 1 4
RFA_00763 0.43 0.42 0.45 5 892 7 1 5 1 7
RFA_00764 0.43 0.42 0.45 5 892 7 1 5 1 7
RFA_00765 0.81 0.67 1.00 8 895 2 0 0 2 4
RFA_00767 0.54 0.50 0.60 9 1876 6 2 4 0 9
RFA_00768 0.50 0.44 0.57 8 1877 9 0 6 3 10
RFA_00769 0.38 0.39 0.39 7 1935 11 2 9 0 11
RFA_00770 0.45 0.39 0.54 7 2003 9 0 6 3 11
RFA_00773 0.45 0.39 0.54 7 1940 9 0 6 3 11
RFA_00779 0.63 0.56 0.71 10 1939 4 3 1 0 8
RFA_00808 -0.01 0.00 0.00 0 1999 19 3 14 2 16
RFA_00809 0.38 0.38 0.40 6 2130 11 0 9 2 10
SPR_00020 0.79 0.75 0.83 15 2683 6 0 3 3 5
SPR_00137 0.84 0.86 0.82 18 2904 10 0 4 6 3
SPR_00273 0.23 0.24 0.24 5 2829 17 0 16 1 16
SPR_00394 0.57 0.57 0.57 12 3634 14 5 4 5 9
SPR_00402 0.62 0.62 0.62 13 2535 8 1 7 0 8
SPR_00721 0.52 0.57 0.48 12 2901 15 1 12 2 9
SPR_00816 0.32 0.35 0.29 7 3462 20 5 12 3 13
SRP_00137 0.36 0.40 0.33 10 4156 22 3 17 2 15
SRP_00285 0.77 0.73 0.81 22 3714 6 0 5 1 8
SRP_00341 -0.01 0.00 0.00 0 4726 27 5 22 0 31

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Performance of Carnac(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for Carnac(seed)

Total Base Pair Counts
Total TP 398
Total TN 149793
Total FP 87
Total FP CONTRA 4
Total FP INCONS 37
Total FP COMP 46
Total FN 1017
Total Scores
MCC 0.503
Average MCC ± 95% Confidence Intervals 0.387 ± 0.084
Sensitivity 0.281
Positive Predictive Value 0.907
Nr of predictions 89

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2. Individual counts for Carnac(seed) [ download as .csv ]

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
PDB_00005 0.88 0.79 1.00 11 935 0 0 0 0 3
PDB_00012 1.00 1.00 1.00 7 399 3 0 0 3 0
PDB_00553 0.79 0.64 1.00 7 458 0 0 0 0 4
PDB_00716 0.00 0.00 0.00 0 2701 0 0 0 0 23
PDB_00810 0.64 0.41 1.00 7 1074 0 0 0 0 10
PDB_01001 0.00 0.00 0.00 0 2145 0 0 0 0 18
PDB_01050 0.62 0.38 1.00 5 625 1 0 0 1 8
PDB_01051 0.00 0.00 0.00 0 903 0 0 0 0 13
PDB_01152 0.88 0.79 1.00 11 550 0 0 0 0 3
RFA_00389 1.00 1.00 1.00 15 1416 2 0 0 2 0
RFA_00390 1.00 1.00 1.00 15 1416 2 0 0 2 0
RFA_00391 0.93 0.87 1.00 13 1418 2 0 0 2 2
RFA_00409 0.77 0.60 1.00 9 1422 1 0 0 1 6
RFA_00416 0.93 0.93 0.93 14 1470 4 0 1 3 1
RFA_00433 1.00 1.00 1.00 15 1416 2 0 0 2 0
RFA_00434 1.00 1.00 1.00 15 1416 2 0 0 2 0
RFA_00436 1.00 1.00 1.00 15 1416 2 0 0 2 0
RFA_00440 1.00 1.00 1.00 15 1470 2 0 0 2 0
RFA_00442 1.00 1.00 1.00 15 1416 2 0 0 2 0
RFA_00446 0.97 0.93 1.00 14 1471 2 0 0 2 1
RFA_00449 0.97 0.93 1.00 14 1471 2 0 0 2 1
RFA_00587 0.00 0.00 0.00 0 4851 0 0 0 0 15
RFA_00632 0.00 0.00 0.00 0 4095 0 0 0 0 28
RFA_00636 0.00 0.00 0.00 0 4005 0 0 0 0 28
RFA_00642 0.00 0.00 0.00 0 2926 0 0 0 0 18
RFA_00643 0.00 0.00 0.00 0 2211 0 0 0 0 18
RFA_00644 0.00 0.00 0.00 0 2701 0 0 0 0 18
RFA_00645 0.00 0.00 0.00 0 2415 0 0 0 0 18
RFA_00649 0.00 0.00 0.00 0 2145 0 0 0 0 18
RFA_00651 0.00 0.00 0.00 0 2080 0 0 0 0 18
RFA_00653 0.00 0.00 0.00 0 2145 0 0 0 0 18
RFA_00654 0.00 0.00 0.00 0 2415 0 0 0 0 18
RFA_00658 0.40 0.29 0.57 4 1121 5 0 3 2 10
RFA_00659 -0.01 0.00 0.00 0 1124 4 0 4 0 14
RFA_00664 0.00 0.00 0.00 0 990 0 0 0 0 14
RFA_00667 -0.01 0.00 0.00 0 985 5 1 4 0 14
RFA_00668 0.50 0.43 0.60 6 980 4 0 4 0 8
RFA_00672 0.00 0.00 0.00 0 903 0 0 0 0 13
RFA_00673 0.47 0.36 0.63 5 1120 4 0 3 1 9
RFA_00674 0.00 0.00 0.00 0 1128 0 0 0 0 14
RFA_00675 0.00 0.00 0.00 0 990 0 0 0 0 14
RFA_00677 0.53 0.43 0.67 6 981 4 0 3 1 8
RFA_00678 0.00 0.00 0.00 0 946 0 0 0 0 14
RFA_00680 0.84 0.71 1.00 10 1118 2 0 0 2 4
RFA_00684 0.84 0.71 1.00 10 980 1 0 0 1 4
RFA_00685 0.59 0.36 1.00 5 985 0 0 0 0 9
RFA_00703 0.00 0.00 0.00 0 4278 0 0 0 0 14
RFA_00704 0.00 0.00 0.00 0 990 0 0 0 0 14
RFA_00705 0.84 0.71 1.00 10 1025 0 0 0 0 4
RFA_00706 0.53 0.29 1.00 4 1031 0 0 0 0 10
RFA_00707 0.53 0.29 1.00 4 1031 0 0 0 0 10
RFA_00708 0.00 0.00 0.00 0 1035 0 0 0 0 14
RFA_00709 -0.01 0.00 0.00 0 984 7 0 6 1 14
RFA_00710 -0.01 0.00 0.00 0 987 3 0 3 0 14
RFA_00711 -0.01 0.00 0.00 0 1031 4 0 4 0 14
RFA_00715 -0.01 0.00 0.00 0 943 3 1 2 0 14
RFA_00716 0.00 0.00 0.00 0 946 0 0 0 0 14
RFA_00717 0.00 0.00 0.00 0 903 0 0 0 0 14
RFA_00730 0.64 0.42 1.00 5 898 1 0 0 1 7
RFA_00731 0.64 0.42 1.00 5 898 1 0 0 1 7
RFA_00733 0.64 0.42 1.00 5 898 1 0 0 1 7
RFA_00734 0.64 0.42 1.00 5 898 0 0 0 0 7
RFA_00736 0.64 0.42 1.00 5 898 1 0 0 1 7
RFA_00737 0.64 0.42 1.00 5 898 1 0 0 1 7
RFA_00745 0.64 0.42 1.00 5 941 1 0 0 1 7
RFA_00749 0.64 0.42 1.00 5 898 1 0 0 1 7
RFA_00758 0.00 0.00 0.00 0 903 0 0 0 0 12
RFA_00762 0.64 0.42 1.00 5 898 0 0 0 0 7
RFA_00763 0.64 0.42 1.00 5 898 1 0 0 1 7
RFA_00764 0.64 0.42 1.00 5 898 1 0 0 1 7
RFA_00765 0.64 0.42 1.00 5 898 1 0 0 1 7
RFA_00767 0.74 0.56 1.00 10 1881 0 0 0 0 8
RFA_00768 0.74 0.56 1.00 10 1881 0 0 0 0 8
RFA_00769 0.71 0.56 0.91 10 1942 1 1 0 0 8
RFA_00770 0.62 0.39 1.00 7 2009 0 0 0 0 11
RFA_00773 0.71 0.56 0.91 10 1942 1 1 0 0 8
RFA_00779 0.74 0.56 1.00 10 1943 0 0 0 0 8
RFA_00808 0.00 0.00 0.00 0 2016 0 0 0 0 16
RFA_00809 0.00 0.00 0.00 0 2145 0 0 0 0 16
SPR_00020 0.00 0.00 0.00 0 2701 0 0 0 0 20
SPR_00137 0.00 0.00 0.00 0 2926 0 0 0 0 21
SPR_00273 0.00 0.00 0.00 0 2850 0 0 0 0 21
SPR_00394 0.00 0.00 0.00 0 3655 0 0 0 0 21
SPR_00402 0.00 0.00 0.00 0 2556 0 0 0 0 21
SPR_00721 0.00 0.00 0.00 0 2926 0 0 0 0 21
SPR_00816 0.00 0.00 0.00 0 3486 0 0 0 0 20
SRP_00137 0.00 0.00 0.00 0 4186 0 0 0 0 25
SRP_00285 0.00 0.00 0.00 0 3741 0 0 0 0 30
SRP_00341 0.00 0.00 0.00 0 4753 0 0 0 0 31

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