CompaRNA - on-line benchmarks of RNA structure prediction methods
Home

Methods
Datasets
Rankings
RNA 2D Atlas

Help
FAQ

Contact us
RSS feeds
Twitter

Table of contents:

  1. Overview

  2. Performance Plots

  3. Performance of RNASampler(seed) - scored higher in this pairwise comparison

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

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


Overview

Metric RNASampler(seed) Afold
MCC 0.634 > 0.602
Average MCC ± 95% Confidence Intervals 0.468 ± 0.070 < 0.585 ± 0.056
Sensitivity 0.471 < 0.593
Positive Predictive Value 0.856 > 0.615
Total TP 995 < 1252
Total TN 648186 > 647313
Total FP 292 < 1147
Total FP CONTRA 52 < 155
Total FP INCONS 116 < 629
Total FP COMP 124 < 363
Total FN 1118 > 861
P-value 3.56938820447e-08

^top




Performance plots


  1. Comparison of performance of RNASampler(seed) and Afold. 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 RNASampler(seed) and Afold).

  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 RNASampler(seed) and Afold).

  3. Comparison of average Matthews Correlation Coefficients (MCCs) for RNASampler(seed) and Afold. 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 RNASampler(seed) and Afold).

^top





Performance of RNASampler(seed) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP 995
Total TN 648186
Total FP 292
Total FP CONTRA 52
Total FP INCONS 116
Total FP COMP 124
Total FN 1118
Total Scores
MCC 0.634
Average MCC ± 95% Confidence Intervals 0.468 ± 0.070
Sensitivity 0.471
Positive Predictive Value 0.856
Nr of predictions 90

^top



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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
PDB_00012 1.00 1.00 1.00 7 399 3 0 0 3 0
PDB_00213 0.76 0.59 1.00 24 5026 0 0 0 0 17
PDB_00553 1.00 1.00 1.00 11 454 0 0 0 0 0
PDB_00716 0.50 0.39 0.64 9 2687 6 0 5 1 14
PDB_00810 0.42 0.18 1.00 3 1078 0 0 0 0 14
PDB_01050 0.92 0.85 1.00 11 619 2 0 0 2 2
PDB_01051 0.45 0.31 0.67 4 897 6 0 2 4 9
PDB_01092 0.72 0.62 0.84 32 10115 8 0 6 2 20
PDB_01152 0.84 0.71 1.00 10 551 0 0 0 0 4
RFA_00390 0.00 0.00 0.00 0 1431 0 0 0 0 15
RFA_00416 0.63 0.40 1.00 6 1479 1 0 0 1 9
RFA_00433 0.63 0.40 1.00 6 1425 1 0 0 1 9
RFA_00587 1.00 1.00 1.00 15 4836 5 0 0 5 0
RFA_00603 0.63 0.51 0.78 18 13507 8 3 2 3 17
RFA_00604 0.73 0.66 0.82 23 13502 14 4 1 9 12
RFA_00606 0.44 0.36 0.54 14 21295 18 7 5 6 25
RFA_00607 0.71 0.56 0.91 20 17744 9 0 2 7 16
RFA_00609 0.82 0.68 1.00 25 17930 6 0 0 6 12
RFA_00610 0.81 0.70 0.93 26 17177 9 0 2 7 11
RFA_00611 0.68 0.57 0.80 20 13016 8 3 2 3 15
RFA_00613 0.58 0.46 0.73 16 12858 6 4 2 0 19
RFA_00615 0.63 0.51 0.78 18 13343 5 3 2 0 17
RFA_00620 0.52 0.44 0.63 17 21918 15 2 8 5 22
RFA_00626 0.80 0.64 1.00 56 56560 5 0 0 5 31
RFA_00627 0.77 0.63 0.93 55 56894 8 0 4 4 32
RFA_00628 0.78 0.64 0.95 55 57233 12 0 3 9 31
RFA_00630 0.77 0.66 0.90 57 56890 15 0 6 9 30
RFA_00632 0.78 0.68 0.90 19 4074 2 1 1 0 9
RFA_00636 0.85 0.75 0.95 21 3983 1 1 0 0 7
RFA_00644 0.44 0.33 0.60 6 2691 4 1 3 0 12
RFA_00645 -0.01 0.00 0.00 0 2403 12 3 9 0 18
RFA_00649 0.44 0.33 0.60 6 2135 4 1 3 0 12
RFA_00653 -0.01 0.00 0.00 0 2133 12 3 9 0 18
RFA_00654 0.39 0.28 0.56 5 2406 4 1 3 0 13
RFA_00658 0.00 0.00 0.00 0 1128 0 0 0 0 14
RFA_00659 0.00 0.00 0.00 0 1128 0 0 0 0 14
RFA_00664 0.00 0.00 0.00 0 990 0 0 0 0 14
RFA_00667 0.53 0.29 1.00 4 986 0 0 0 0 10
RFA_00668 0.00 0.00 0.00 0 990 0 0 0 0 14
RFA_00672 0.00 0.00 0.00 0 903 0 0 0 0 13
RFA_00673 0.00 0.00 0.00 0 1128 0 0 0 0 14
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 0.00 0.00 0.00 0 990 0 0 0 0 14
RFA_00678 0.00 0.00 0.00 0 946 0 0 0 0 14
RFA_00680 0.00 0.00 0.00 0 1128 0 0 0 0 14
RFA_00684 0.53 0.29 1.00 4 986 0 0 0 0 10
RFA_00685 0.00 0.00 0.00 0 990 0 0 0 0 14
RFA_00695 0.00 0.00 0.00 0 7021 0 0 0 0 14
RFA_00703 0.46 0.21 1.00 3 4275 0 0 0 0 11
RFA_00704 -0.01 0.00 0.00 0 987 3 0 3 0 14
RFA_00705 0.00 0.00 0.00 0 1035 0 0 0 0 14
RFA_00706 0.00 0.00 0.00 0 1035 0 0 0 0 14
RFA_00707 0.00 0.00 0.00 0 1035 0 0 0 0 14
RFA_00708 0.00 0.00 0.00 0 1035 0 0 0 0 14
RFA_00709 0.00 0.00 0.00 0 990 0 0 0 0 14
RFA_00710 0.00 0.00 0.00 0 990 0 0 0 0 14
RFA_00711 0.00 0.00 0.00 0 1035 0 0 0 0 14
RFA_00716 -0.01 0.00 0.00 0 943 3 0 3 0 14
RFA_00717 0.00 0.00 0.00 0 903 0 0 0 0 14
RFA_00730 0.50 0.25 1.00 3 900 0 0 0 0 9
RFA_00731 0.64 0.42 1.00 5 898 1 0 0 1 7
RFA_00733 0.50 0.25 1.00 3 900 0 0 0 0 9
RFA_00734 0.64 0.42 1.00 5 898 0 0 0 0 7
RFA_00736 0.50 0.25 1.00 3 900 0 0 0 0 9
RFA_00737 0.64 0.42 1.00 5 898 1 0 0 1 7
RFA_00745 0.50 0.25 1.00 3 943 0 0 0 0 9
RFA_00749 0.50 0.25 1.00 3 900 0 0 0 0 9
RFA_00758 0.50 0.25 1.00 3 900 0 0 0 0 9
RFA_00762 0.64 0.42 1.00 5 898 0 0 0 0 7
RFA_00763 0.50 0.25 1.00 3 900 0 0 0 0 9
RFA_00764 0.50 0.25 1.00 3 900 0 0 0 0 9
RFA_00765 0.50 0.25 1.00 3 900 0 0 0 0 9
RFA_00767 0.65 0.56 0.77 10 1878 3 3 0 0 8
RFA_00768 0.65 0.56 0.77 10 1878 3 3 0 0 8
RFA_00769 0.59 0.56 0.63 10 1937 6 1 5 0 8
RFA_00770 0.52 0.39 0.70 7 2006 3 3 0 0 11
RFA_00773 0.59 0.50 0.69 9 1940 4 4 0 0 9
RFA_00781 0.85 0.72 1.00 23 5027 0 0 0 0 9
RFA_00786 0.79 0.63 1.00 20 5030 0 0 0 0 12
RFA_00791 0.71 0.56 0.90 18 5131 2 0 2 0 14
RFA_00792 0.81 0.72 0.92 23 5025 2 0 2 0 9
RFA_00801 0.74 0.63 0.87 20 5027 4 0 3 1 12
RFA_00808 0.58 0.56 0.60 9 2001 6 0 6 0 7
RFA_00809 0.36 0.38 0.35 6 2128 11 1 10 0 10
RFA_00814 0.87 0.78 0.97 32 25167 6 0 1 5 9
RFA_00815 0.88 0.78 1.00 32 24499 8 0 0 8 9
RFA_00816 0.86 0.76 0.97 31 23188 6 0 1 5 10
RFA_00818 0.86 0.73 1.00 30 20271 6 0 0 6 11
RFA_00819 0.88 0.78 1.00 32 27934 5 0 0 5 9

^top



Performance of Afold - scored lower in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP 1252
Total TN 647313
Total FP 1147
Total FP CONTRA 155
Total FP INCONS 629
Total FP COMP 363
Total FN 861
Total Scores
MCC 0.602
Average MCC ± 95% Confidence Intervals 0.585 ± 0.056
Sensitivity 0.593
Positive Predictive Value 0.615
Nr of predictions 90

^top



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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
PDB_00012 1.00 1.00 1.00 7 399 3 0 0 3 0
PDB_00213 0.87 0.80 0.94 33 5015 2 0 2 0 8
PDB_00553 1.00 1.00 1.00 11 454 0 0 0 0 0
PDB_00716 -0.01 0.00 0.00 0 2677 25 1 23 1 23
PDB_00810 0.77 0.71 0.86 12 1067 2 0 2 0 5
PDB_01050 0.96 0.92 1.00 12 618 2 0 0 2 1
PDB_01051 0.75 0.69 0.82 9 892 6 0 2 4 4
PDB_01092 0.69 0.60 0.79 31 10114 11 1 7 3 21
PDB_01152 0.96 0.93 1.00 13 548 0 0 0 0 1
RFA_00390 1.00 1.00 1.00 15 1416 2 0 0 2 0
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_00587 0.87 0.87 0.87 13 4836 14 0 2 12 2
RFA_00603 0.64 0.69 0.60 24 13490 20 4 12 4 11
RFA_00604 0.72 0.74 0.70 26 13493 24 2 9 13 9
RFA_00606 0.67 0.67 0.68 26 21283 26 7 5 14 13
RFA_00607 0.57 0.61 0.54 22 17725 25 6 13 6 14
RFA_00609 0.75 0.76 0.74 28 17917 28 2 8 18 9
RFA_00610 0.77 0.76 0.78 28 17169 23 2 6 15 9
RFA_00611 0.79 0.77 0.82 27 13008 13 0 6 7 8
RFA_00613 0.61 0.60 0.62 21 12846 17 4 9 4 14
RFA_00615 0.51 0.51 0.51 18 13331 18 8 9 1 17
RFA_00620 0.64 0.62 0.67 24 21909 26 3 9 14 15
RFA_00626 0.89 0.86 0.93 75 56535 31 2 4 25 12
RFA_00627 0.48 0.47 0.48 41 56868 50 10 34 6 46
RFA_00628 0.83 0.80 0.85 69 57210 38 1 11 26 17
RFA_00630 0.60 0.60 0.60 52 56866 46 8 27 11 35
RFA_00632 0.40 0.39 0.41 11 4068 18 0 16 2 17
RFA_00636 0.42 0.43 0.43 12 3977 17 2 14 1 16
RFA_00644 -0.01 0.00 0.00 0 2681 21 4 16 1 18
RFA_00645 -0.01 0.00 0.00 0 2401 15 3 11 1 18
RFA_00649 0.65 0.61 0.69 11 2129 8 1 4 3 7
RFA_00653 0.34 0.33 0.35 6 2128 12 3 8 1 12
RFA_00654 0.27 0.28 0.28 5 2397 14 2 11 1 13
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 1 7 2 10
RFA_00664 0.07 0.07 0.09 1 979 11 0 10 1 13
RFA_00667 0.30 0.29 0.33 4 978 8 1 7 0 10
RFA_00668 0.41 0.43 0.40 6 975 9 0 9 0 8
RFA_00672 0.17 0.15 0.20 2 893 9 0 8 1 11
RFA_00673 0.42 0.36 0.50 5 1118 6 0 5 1 9
RFA_00674 0.69 0.71 0.67 10 1113 6 0 5 1 4
RFA_00675 0.29 0.29 0.31 4 977 9 1 8 0 10
RFA_00677 0.42 0.43 0.43 6 976 9 0 8 1 8
RFA_00678 0.66 0.64 0.69 9 933 4 0 4 0 5
RFA_00680 0.74 0.71 0.77 10 1115 6 0 3 3 4
RFA_00684 0.66 0.64 0.69 9 977 5 0 4 1 5
RFA_00685 0.42 0.36 0.50 5 980 6 0 5 1 9
RFA_00695 0.67 0.64 0.69 9 7008 29 1 3 25 5
RFA_00703 0.67 0.64 0.69 9 4265 18 1 3 14 5
RFA_00704 0.48 0.43 0.55 6 979 7 0 5 2 8
RFA_00705 0.69 0.71 0.67 10 1020 5 0 5 0 4
RFA_00706 0.44 0.36 0.56 5 1026 4 0 4 0 9
RFA_00707 0.07 0.07 0.10 1 1025 9 3 6 0 13
RFA_00708 0.47 0.36 0.63 5 1027 3 0 3 0 9
RFA_00709 0.16 0.14 0.20 2 980 9 0 8 1 12
RFA_00710 0.23 0.21 0.27 3 979 8 0 8 0 11
RFA_00711 0.40 0.36 0.45 5 1024 6 0 6 0 9
RFA_00716 0.06 0.07 0.08 1 933 12 0 12 0 13
RFA_00717 0.64 0.64 0.64 9 889 5 0 5 0 5
RFA_00730 0.69 0.67 0.73 8 892 4 1 2 1 4
RFA_00731 0.66 0.67 0.67 8 891 5 1 3 1 4
RFA_00733 0.66 0.67 0.67 8 891 5 1 3 1 4
RFA_00734 0.61 0.67 0.57 8 889 8 1 5 2 4
RFA_00736 0.66 0.67 0.67 8 891 5 1 3 1 4
RFA_00737 1.00 1.00 1.00 12 891 1 0 0 1 0
RFA_00745 0.66 0.67 0.67 8 934 5 1 3 1 4
RFA_00749 0.66 0.67 0.67 8 891 5 1 3 1 4
RFA_00758 0.96 0.92 1.00 11 892 1 0 0 1 1
RFA_00762 0.64 0.67 0.62 8 890 6 1 4 1 4
RFA_00763 1.00 1.00 1.00 12 891 1 0 0 1 0
RFA_00764 0.66 0.67 0.67 8 891 5 1 3 1 4
RFA_00765 1.00 1.00 1.00 12 891 1 0 0 1 0
RFA_00767 0.63 0.56 0.71 10 1877 5 0 4 1 8
RFA_00768 0.48 0.44 0.53 8 1876 8 1 6 1 10
RFA_00769 0.55 0.56 0.56 10 1935 10 3 5 2 8
RFA_00770 0.68 0.56 0.83 10 2004 6 0 2 4 8
RFA_00773 0.71 0.56 0.91 10 1942 5 1 0 4 8
RFA_00781 0.55 0.56 0.55 18 5017 17 2 13 2 14
RFA_00786 0.71 0.72 0.70 23 5017 12 2 8 2 9
RFA_00791 0.50 0.50 0.52 16 5120 16 3 12 1 16
RFA_00792 0.90 0.88 0.93 28 5020 3 0 2 1 4
RFA_00801 0.59 0.59 0.59 19 5018 14 0 13 1 13
RFA_00808 -0.01 0.00 0.00 0 2001 16 2 13 1 16
RFA_00809 0.36 0.38 0.35 6 2128 12 1 10 1 10
RFA_00814 0.35 0.37 0.33 15 25155 42 7 23 12 26
RFA_00815 0.56 0.61 0.51 25 24482 35 8 16 11 16
RFA_00816 0.59 0.66 0.53 27 23169 33 13 11 9 14
RFA_00818 0.19 0.22 0.17 9 20247 48 19 26 3 32
RFA_00819 0.96 0.95 0.98 39 27926 32 0 1 31 2

^top


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