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

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric HotKnots Murlet(seed)
MCC 0.572 > 0.477
Average MCC ± 95% Confidence Intervals 0.539 ± 0.070 > 0.348 ± 0.081
Sensitivity 0.562 > 0.277
Positive Predictive Value 0.588 < 0.828
Total TP 963 > 475
Total TN 275688 < 276752
Total FP 832 > 103
Total FP CONTRA 93 > 0
Total FP INCONS 582 > 99
Total FP COMP 157 > 4
Total FN 752 < 1240
P-value 3.56938820447e-08

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Performance plots


  1. Comparison of performance of HotKnots and Murlet(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 HotKnots and Murlet(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 HotKnots and Murlet(seed)).

  3. Comparison of average Matthews Correlation Coefficients (MCCs) for HotKnots and Murlet(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 HotKnots and Murlet(seed)).

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Performance of HotKnots - scored higher in this pairwise comparison

1. Total counts & total scores for HotKnots

Total Base Pair Counts
Total TP 963
Total TN 275688
Total FP 832
Total FP CONTRA 93
Total FP INCONS 582
Total FP COMP 157
Total FN 752
Total Scores
MCC 0.572
Average MCC ± 95% Confidence Intervals 0.539 ± 0.070
Sensitivity 0.562
Positive Predictive Value 0.588
Nr of predictions 89

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2. Individual counts for HotKnots [ 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_00213 0.92 0.85 1.00 35 5015 0 0 0 0 6
PDB_00553 1.00 1.00 1.00 11 454 0 0 0 0 0
PDB_00716 -0.01 0.00 0.00 0 2678 24 1 22 1 23
PDB_00810 0.71 0.65 0.79 11 1067 4 0 3 1 6
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 0.65 0.74 34 10107 13 0 12 1 18
PDB_01152 0.92 0.86 1.00 12 549 0 0 0 0 2
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 1.00 1.00 1.00 15 4836 12 0 0 12 0
RFA_00603 0.64 0.69 0.60 24 13490 19 4 12 3 11
RFA_00604 0.72 0.74 0.70 26 13493 22 2 9 11 9
RFA_00605 0.37 0.34 0.40 12 15195 27 3 15 9 23
RFA_00611 0.63 0.63 0.63 22 13006 15 3 10 2 13
RFA_00613 0.61 0.60 0.62 21 12846 15 4 9 2 14
RFA_00615 0.51 0.51 0.51 18 13331 17 8 9 0 17
RFA_00620 0.64 0.62 0.67 24 21909 25 3 9 13 15
RFA_00632 0.38 0.39 0.37 11 4065 19 2 17 0 17
RFA_00636 0.42 0.43 0.43 12 3977 16 2 14 0 16
RFA_00642 0.16 0.17 0.17 3 2908 15 1 14 0 15
RFA_00643 0.20 0.22 0.20 4 2191 16 1 15 0 14
RFA_00644 -0.01 0.00 0.00 0 2676 25 6 19 0 18
RFA_00645 -0.01 0.00 0.00 0 2394 21 4 17 0 18
RFA_00649 0.34 0.33 0.35 6 2128 13 2 9 2 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 11 3 8 0 12
RFA_00654 0.27 0.28 0.28 5 2397 13 2 11 0 13
RFA_00658 0.59 0.50 0.70 7 1118 5 0 3 2 7
RFA_00659 -0.01 0.00 0.00 0 1120 10 1 7 2 14
RFA_00664 -0.01 0.00 0.00 0 980 11 0 10 1 14
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 -0.01 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 0.71 0.71 0.71 10 1114 5 0 4 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 0.43 0.29 0.67 4 940 2 0 2 0 10
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 0.56 0.50 0.64 7 7010 29 1 3 25 7
RFA_00703 0.67 0.64 0.69 9 4265 18 1 3 14 5
RFA_00704 -0.01 0.00 0.00 0 976 14 2 12 0 14
RFA_00705 0.69 0.71 0.67 10 1020 5 0 5 0 4
RFA_00706 0.29 0.29 0.31 4 1022 10 0 9 1 10
RFA_00707 -0.01 0.00 0.00 0 1026 9 3 6 0 14
RFA_00708 0.30 0.29 0.33 4 1023 10 0 8 2 10
RFA_00709 -0.01 0.00 0.00 0 981 10 0 9 1 14
RFA_00710 -0.01 0.00 0.00 0 981 9 0 9 0 14
RFA_00711 -0.01 0.00 0.00 0 1026 10 0 9 1 14
RFA_00715 -0.01 0.00 0.00 0 936 10 0 10 0 14
RFA_00716 -0.01 0.00 0.00 0 935 11 0 11 0 14
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 7 1 5 1 4
RFA_00736 0.66 0.67 0.67 8 891 5 1 3 1 4
RFA_00737 0.75 0.75 0.75 9 891 5 0 3 2 3
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 0.63 0.58 0.70 7 893 3 1 2 0 5
RFA_00762 0.64 0.67 0.62 8 890 5 1 4 0 4
RFA_00763 0.75 0.75 0.75 9 891 4 0 3 1 3
RFA_00764 0.66 0.67 0.67 8 891 5 1 3 1 4
RFA_00765 0.75 0.75 0.75 9 891 5 0 3 2 3
RFA_00767 0.93 1.00 0.86 18 1870 3 3 0 0 0
RFA_00768 1.00 1.00 1.00 18 1873 0 0 0 0 0
RFA_00769 -0.01 0.00 0.00 0 1934 21 0 19 2 18
RFA_00770 -0.01 0.00 0.00 0 1999 20 0 17 3 18
RFA_00773 -0.01 0.00 0.00 0 1934 22 0 19 3 18
RFA_00779 0.87 0.94 0.81 17 1932 4 3 1 0 1
RFA_00781 0.58 0.59 0.58 19 5017 14 2 12 0 13
RFA_00786 0.71 0.72 0.70 23 5017 10 2 8 0 9
RFA_00791 0.35 0.34 0.35 11 5120 20 5 15 0 21
RFA_00792 0.94 0.94 0.94 30 5018 4 0 2 2 2
RFA_00801 0.85 0.81 0.90 26 5021 4 0 3 1 6
RFA_00808 1.00 1.00 1.00 16 2000 0 0 0 0 0
RFA_00809 0.79 0.81 0.76 13 2128 4 0 4 0 3
SRP_00137 0.74 0.84 0.66 21 4154 13 4 7 2 4
SRP_00141 0.91 0.90 0.93 37 6288 3 1 2 0 4
SRP_00146 0.93 0.94 0.92 34 5216 3 1 2 0 2
SRP_00285 0.91 0.87 0.96 26 3714 1 0 1 0 4
SRP_00338 0.94 0.94 0.94 34 5424 2 0 2 0 2

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

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

Total Base Pair Counts
Total TP 475
Total TN 276752
Total FP 103
Total FP CONTRA 0
Total FP INCONS 99
Total FP COMP 4
Total FN 1240
Total Scores
MCC 0.477
Average MCC ± 95% Confidence Intervals 0.348 ± 0.081
Sensitivity 0.277
Positive Predictive Value 0.828
Nr of predictions 89

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
PDB_00005 0.53 0.29 1.00 4 942 2 0 0 2 10
PDB_00012 0.65 0.43 1.00 3 403 0 0 0 0 4
PDB_00213 0.73 0.59 0.92 24 5024 2 0 2 0 17
PDB_00553 0.45 0.27 0.75 3 461 1 0 1 0 8
PDB_00716 0.23 0.13 0.43 3 2694 4 0 4 0 20
PDB_00810 0.63 0.53 0.75 9 1069 3 0 3 0 8
PDB_01050 0.55 0.31 1.00 4 626 1 0 0 1 9
PDB_01051 0.00 0.00 0.00 0 903 0 0 0 0 13
PDB_01092 0.69 0.48 1.00 25 10128 0 0 0 0 27
PDB_01152 0.76 0.64 0.90 9 551 1 0 1 0 5
RFA_00390 0.00 0.00 0.00 0 1431 0 0 0 0 15
RFA_00416 0.00 0.00 0.00 0 1485 0 0 0 0 15
RFA_00433 0.00 0.00 0.00 0 1431 0 0 0 0 15
RFA_00587 0.00 0.00 0.00 0 4851 0 0 0 0 15
RFA_00603 0.00 0.00 0.00 0 13530 0 0 0 0 35
RFA_00604 0.00 0.00 0.00 0 13530 0 0 0 0 35
RFA_00605 0.00 0.00 0.00 0 15225 0 0 0 0 35
RFA_00611 0.00 0.00 0.00 0 13041 0 0 0 0 35
RFA_00613 0.00 0.00 0.00 0 12880 0 0 0 0 35
RFA_00615 0.00 0.00 0.00 0 13366 0 0 0 0 35
RFA_00620 0.00 0.00 0.00 0 21945 0 0 0 0 39
RFA_00632 0.21 0.11 0.43 3 4088 4 0 4 0 25
RFA_00636 0.21 0.11 0.43 3 3998 4 0 4 0 25
RFA_00642 0.57 0.44 0.73 8 2915 3 0 3 0 10
RFA_00643 -0.01 0.00 0.00 0 2203 8 0 8 0 18
RFA_00644 0.42 0.33 0.55 6 2690 5 0 5 0 12
RFA_00645 0.00 0.00 0.00 0 2407 8 0 8 0 18
RFA_00649 -0.01 0.00 0.00 0 2137 8 0 8 0 18
RFA_00651 0.42 0.33 0.55 6 2069 5 0 5 0 12
RFA_00653 -0.01 0.00 0.00 0 2137 8 0 8 0 18
RFA_00654 0.57 0.44 0.73 8 2404 3 0 3 0 10
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 0.00 0.00 0.00 0 990 0 0 0 0 14
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 0.00 0.00 0.00 0 990 0 0 0 0 14
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 0.00 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 0.00 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_00715 0.00 0.00 0.00 0 946 0 0 0 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 1.00 1.00 1.00 12 891 0 0 0 0 0
RFA_00731 1.00 1.00 1.00 12 891 0 0 0 0 0
RFA_00733 1.00 1.00 1.00 12 891 0 0 0 0 0
RFA_00734 1.00 1.00 1.00 12 891 0 0 0 0 0
RFA_00736 1.00 1.00 1.00 12 891 0 0 0 0 0
RFA_00737 1.00 1.00 1.00 12 891 0 0 0 0 0
RFA_00745 1.00 1.00 1.00 12 934 0 0 0 0 0
RFA_00749 1.00 1.00 1.00 12 891 0 0 0 0 0
RFA_00758 1.00 1.00 1.00 12 891 0 0 0 0 0
RFA_00762 1.00 1.00 1.00 12 891 0 0 0 0 0
RFA_00763 1.00 1.00 1.00 12 891 0 0 0 0 0
RFA_00764 1.00 1.00 1.00 12 891 0 0 0 0 0
RFA_00765 1.00 1.00 1.00 12 891 0 0 0 0 0
RFA_00767 0.47 0.33 0.67 6 1882 3 0 3 0 12
RFA_00768 0.41 0.28 0.63 5 1883 3 0 3 0 13
RFA_00769 0.57 0.44 0.73 8 1942 3 0 3 0 10
RFA_00770 0.57 0.44 0.73 8 2005 3 0 3 0 10
RFA_00773 0.41 0.28 0.63 5 1945 3 0 3 0 13
RFA_00779 0.47 0.33 0.67 6 1944 3 0 3 0 12
RFA_00781 0.83 0.75 0.92 24 5024 2 0 2 0 8
RFA_00786 0.83 0.75 0.92 24 5024 2 0 2 0 8
RFA_00791 0.83 0.75 0.92 24 5125 2 0 2 0 8
RFA_00792 0.83 0.75 0.92 24 5024 2 0 2 0 8
RFA_00801 0.80 0.72 0.88 23 5024 3 0 3 0 9
RFA_00808 0.75 0.56 1.00 9 2007 0 0 0 0 7
RFA_00809 0.50 0.38 0.67 6 2136 3 0 3 0 10
SRP_00137 0.49 0.24 1.00 6 4180 0 0 0 0 19
SRP_00141 0.35 0.12 1.00 5 6323 1 0 0 1 36
SRP_00146 0.41 0.17 1.00 6 5247 0 0 0 0 30
SRP_00285 0.45 0.20 1.00 6 3735 0 0 0 0 24
SRP_00338 0.41 0.17 1.00 6 5454 0 0 0 0 30

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