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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric ContextFold Afold
MCC 0.513 > 0.508
Average MCC ± 95% Confidence Intervals 0.718 ± 0.144 > 0.697 ± 0.137
Sensitivity 0.515 < 0.546
Positive Predictive Value 0.512 > 0.474
Total TP 413 < 438
Total TN 456770 > 456651
Total FP 466 < 594
Total FP CONTRA 96 < 144
Total FP INCONS 297 < 343
Total FP COMP 73 < 107
Total FN 389 > 364
P-value 0.001244508652

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Performance plots


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

  2. Comparison of performance of ContextFold 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 ContextFold and Afold).

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

  4. Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold 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 ContextFold and Afold).

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Performance of ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

Total Base Pair Counts
Total TP 413
Total TN 456770
Total FP 466
Total FP CONTRA 96
Total FP INCONS 297
Total FP COMP 73
Total FN 389
Total Scores
MCC 0.513
Average MCC ± 95% Confidence Intervals 0.718 ± 0.144
Sensitivity 0.515
Positive Predictive Value 0.512
Nr of predictions 28

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2. Individual counts for ContextFold [ 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...

0.58 0.56 0.63 10 512 6 0 6 0 8
2LDL_A - 1.00 1.00 1.00 9 131 0 0 0 0 0
2LHP_A - 1.00 1.00 1.00 15 246 0 0 0 0 0
2LI4_A - 1.00 1.00 1.00 14 175 0 0 0 0 0
2LJJ_A - 0.92 0.86 1.00 6 124 3 0 0 3 1
2LK3_A - 0.94 0.89 1.00 8 92 0 0 0 0 1
2LKR_A - 0.70 0.66 0.76 19 2415 12 0 6 6 10
2LQZ_A - 1.00 1.00 1.00 8 124 1 0 0 1 0
2LWK_A - 1.00 1.00 1.00 11 196 1 0 0 1 0
3J0L_1 - 0.75 0.69 0.82 9 473 5 0 2 3 4
3J0L_h - 0.95 0.91 1.00 29 2111 2 0 0 2 3
3J0L_7 - -0.02 0.00 0.00 0 506 13 3 10 0 10
3J2C_O - 1.00 1.00 1.00 41 3946 4 0 0 4 0
3SN2_B

IRE_II links to Rfam database...

0.95 0.92 1.00 11 143 0 0 0 0 1
3U4M_B - 0.98 0.95 1.00 21 1255 0 0 0 0 1
3VJR_D - 1.00 1.00 1.00 12 239 0 0 0 0 0
3W3S_B

tRNA-Sec links to Rfam database...

0.87 0.85 0.90 28 1958 4 0 3 1 5
3ZEX_F - 0.00 0.00 0.00 0 910 16 0 4 12 4
3ZEX_E - 0.12 0.15 0.10 5 8255 44 20 24 0 29
3ZEX_D

5S_rRNA links to Rfam database...

0.92 0.86 1.00 30 2766 4 0 0 4 5
3ZEX_B - 0.23 0.23 0.23 81 420993 296 62 216 18 265
3ZEX_H - 0.29 0.37 0.24 7 3596 27 7 15 5 12
4A1C_2

5_8S_rRNA links to Rfam database...

0.26 0.25 0.28 5 4498 26 3 10 13 15
4A4U_A - 1.00 1.00 1.00 9 96 0 0 0 0 0
4ATO_G - -0.02 0.00 0.00 0 218 2 1 1 0 7
4ENB_A

crcB links to Rfam database...

0.77 0.60 1.00 9 463 0 0 0 0 6
4FNJ_A - 0.91 0.83 1.00 10 240 0 0 0 0 2
4HXH_A - 1.00 1.00 1.00 6 89 0 0 0 0 0

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Performance of Afold - scored lower in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP 438
Total TN 456651
Total FP 594
Total FP CONTRA 144
Total FP INCONS 343
Total FP COMP 107
Total FN 364
Total Scores
MCC 0.508
Average MCC ± 95% Confidence Intervals 0.697 ± 0.137
Sensitivity 0.546
Positive Predictive Value 0.474
Nr of predictions 28

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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...

0.64 0.61 0.69 11 512 6 0 5 1 7
2LDL_A - 1.00 1.00 1.00 9 131 1 0 0 1 0
2LHP_A - 1.00 1.00 1.00 15 246 0 0 0 0 0
2LI4_A - 1.00 1.00 1.00 14 175 0 0 0 0 0
2LJJ_A - 1.00 1.00 1.00 7 123 3 0 0 3 0
2LK3_A - 1.00 1.00 1.00 9 91 0 0 0 0 0
2LKR_A - 1.00 1.00 1.00 29 2411 8 0 0 8 0
2LQZ_A - 1.00 1.00 1.00 8 124 2 0 0 2 0
2LWK_A - 0.85 0.82 0.90 9 197 2 0 1 1 2
3J0L_1 - 0.83 0.77 0.91 10 473 5 0 1 4 3
3J0L_h - 0.87 0.81 0.93 26 2112 5 1 1 3 6
3J0L_7 - -0.02 0.00 0.00 0 504 15 1 14 0 10
3J2C_O - 0.70 0.68 0.72 28 3948 18 3 8 7 13
3SN2_B

IRE_II links to Rfam database...

0.95 0.92 1.00 11 143 0 0 0 0 1
3U4M_B - 0.49 0.55 0.46 12 1250 14 3 11 0 10
3VJR_D - 1.00 1.00 1.00 12 239 1 0 0 1 0
3W3S_B

tRNA-Sec links to Rfam database...

0.55 0.55 0.56 18 1957 15 4 10 1 15
3ZEX_F - -0.01 0.00 0.00 0 908 12 2 4 6 4
3ZEX_E - -0.01 0.00 0.00 0 8251 55 17 36 2 34
3ZEX_D

5S_rRNA links to Rfam database...

0.82 0.77 0.87 27 2765 8 0 4 4 8
3ZEX_B - 0.34 0.38 0.31 132 420926 337 77 217 43 214
3ZEX_H - 0.25 0.37 0.18 7 3586 33 20 12 1 12
4A1C_2

5_8S_rRNA links to Rfam database...

0.19 0.25 0.15 5 4483 43 11 17 15 15
4A4U_A - 1.00 1.00 1.00 9 96 0 0 0 0 0
4ATO_G - 0.38 0.43 0.38 3 212 6 5 0 1 4
4ENB_A

crcB links to Rfam database...

0.81 0.73 0.92 11 460 3 0 1 2 4
4FNJ_A - 0.86 0.83 0.91 10 239 1 0 1 0 2
4HXH_A - 1.00 1.00 1.00 6 89 1 0 0 1 0

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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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