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 IPknot - scored higher in this pairwise comparison

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

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


Overview

Metric IPknot Afold
MCC 0.664 > 0.567
Average MCC ± 95% Confidence Intervals 0.662 ± 0.397 > 0.609 ± 0.353
Sensitivity 0.626 > 0.596
Positive Predictive Value 0.713 > 0.551
Total TP 62 > 59
Total TN 7571 > 7551
Total FP 34 < 66
Total FP CONTRA 11 < 14
Total FP INCONS 14 < 34
Total FP COMP 9 < 18
Total FN 37 < 40
P-value 0.0

^top



Performance plots


  1. Comparison of performance of IPknot 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 IPknot and Afold).

  2. Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot 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 IPknot and Afold).

^top




Performance of IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP 62
Total TN 7571
Total FP 34
Total FP CONTRA 11
Total FP INCONS 14
Total FP COMP 9
Total FN 37
Total Scores
MCC 0.664
Average MCC ± 95% Confidence Intervals 0.662 ± 0.397
Sensitivity 0.626
Positive Predictive Value 0.713
Nr of predictions 5

^top


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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
2LC8_A

GP_knot1 links to Rfam database...

0.41 0.33 0.55 6 517 5 1 4 0 12
3RKF_A

Purine links to Rfam database...

0.91 0.83 1.00 20 846 0 0 0 0 4
3U4M_B - 0.91 0.91 0.91 20 1254 3 2 0 1 2
4A1C_2

5_8S_rRNA links to Rfam database...

0.23 0.25 0.22 5 4493 26 8 10 8 15
4ENB_A

crcB links to Rfam database...

0.85 0.73 1.00 11 461 0 0 0 0 4

^top


Performance of Afold - scored lower in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP 59
Total TN 7551
Total FP 66
Total FP CONTRA 14
Total FP INCONS 34
Total FP COMP 18
Total FN 40
Total Scores
MCC 0.567
Average MCC ± 95% Confidence Intervals 0.609 ± 0.353
Sensitivity 0.596
Positive Predictive Value 0.551
Nr of predictions 5

^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
2LC8_A

GP_knot1 links to Rfam database...

0.64 0.61 0.69 11 512 6 0 5 1 7
3RKF_A

Purine links to Rfam database...

0.91 0.83 1.00 20 846 0 0 0 0 4
3U4M_B - 0.49 0.55 0.46 12 1250 14 3 11 0 10
4A1C_2

5_8S_rRNA links to Rfam database...

0.19 0.25 0.15 5 4483 43 11 17 15 15
4ENB_A

crcB links to Rfam database...

0.81 0.73 0.92 11 460 3 0 1 2 4

^top

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

Copyright© - Adam Mickiewicz University & IIMCB - All rights reserved