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Table of contents:

  1. Overview

  2. Performance Plots

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

  4. Performance of CentroidHomfold‑LAST - scored lower in this pairwise comparison

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


Overview

Metric Afold CentroidHomfold‑LAST
MCC 0.516 > 0.401
Average MCC ± 95% Confidence Intervals 0.498 ± 0.317 > 0.402 ± 0.314
Sensitivity 0.467 > 0.286
Positive Predictive Value 0.578 > 0.570
Total TP 93 > 57
Total TN 27136 < 27197
Total FP 84 > 49
Total FP CONTRA 7 > 5
Total FP INCONS 61 > 38
Total FP COMP 16 > 6
Total FN 106 < 142
P-value 0.0

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Performance plots


  1. Comparison of performance of Afold and CentroidHomfold-LAST. 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 Afold and CentroidHomfold‑LAST).

  2. Comparison of average Matthews Correlation Coefficients (MCCs) for Afold and CentroidHomfold-LAST. 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 Afold and CentroidHomfold‑LAST).

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Performance of Afold - scored higher in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP 93
Total TN 27136
Total FP 84
Total FP CONTRA 7
Total FP INCONS 61
Total FP COMP 16
Total FN 106
Total Scores
MCC 0.516
Average MCC ± 95% Confidence Intervals 0.498 ± 0.317
Sensitivity 0.467
Positive Predictive Value 0.578
Nr of predictions 7

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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...

0.61 0.55 0.69 11 1524 6 0 5 1 9
2LKR_A - 0.93 0.87 1.00 34 6071 3 0 0 3 5
3J0L_7 - -0.01 0.00 0.00 0 1210 15 1 14 0 17
3RKF_A

Purine links to Rfam database...

0.76 0.59 1.00 20 2191 0 0 0 0 14
3U4M_B - 0.38 0.32 0.46 12 3134 14 0 14 0 25
4A1C_2

5_8S_rRNA links to Rfam database...

0.14 0.15 0.14 5 11745 43 5 26 12 28
4ENB_A

crcB links to Rfam database...

0.67 0.58 0.79 11 1261 3 1 2 0 8

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Performance of CentroidHomfold‑LAST - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidHomfold‑LAST

Total Base Pair Counts
Total TP 57
Total TN 27197
Total FP 49
Total FP CONTRA 5
Total FP INCONS 38
Total FP COMP 6
Total FN 142
Total Scores
MCC 0.401
Average MCC ± 95% Confidence Intervals 0.402 ± 0.314
Sensitivity 0.286
Positive Predictive Value 0.570
Nr of predictions 7

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2. Individual counts for CentroidHomfold‑LAST [ 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...

-0.01 0.00 0.00 0 1529 11 0 11 0 20
2LKR_A - 0.00 0.00 0.00 0 6101 4 0 4 0 39
3J0L_7 - 0.60 0.41 0.88 7 1217 1 0 1 0 10
3RKF_A

Purine links to Rfam database...

0.72 0.53 1.00 18 2193 0 0 0 0 16
3U4M_B - 0.58 0.43 0.80 16 3140 4 0 4 0 21
4A1C_2

5_8S_rRNA links to Rfam database...

0.16 0.15 0.18 5 11753 29 5 18 6 28
4ENB_A

crcB links to Rfam database...

0.76 0.58 1.00 11 1264 0 0 0 0 8

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

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