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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric Alterna NanoFolder
MCC 0.756 > 0.610
Average MCC ± 95% Confidence Intervals 0.803 ± 0.218 > 0.721 ± 0.307
Sensitivity 0.753 > 0.706
Positive Predictive Value 0.771 > 0.545
Total TP 64 > 60
Total TN 3291 > 3264
Total FP 26 < 56
Total FP CONTRA 7 < 19
Total FP INCONS 12 < 31
Total FP COMP 7 > 6
Total FN 21 < 25
P-value 0.0

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Performance plots


  1. Comparison of performance of Alterna and NanoFolder. 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 Alterna and NanoFolder).

  2. Comparison of average Matthews Correlation Coefficients (MCCs) for Alterna and NanoFolder. 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 Alterna and NanoFolder).

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Performance of Alterna - scored higher in this pairwise comparison

1. Total counts & total scores for Alterna

Total Base Pair Counts
Total TP 64
Total TN 3291
Total FP 26
Total FP CONTRA 7
Total FP INCONS 12
Total FP COMP 7
Total FN 21
Total Scores
MCC 0.756
Average MCC ± 95% Confidence Intervals 0.803 ± 0.218
Sensitivity 0.753
Positive Predictive Value 0.771
Nr of predictions 6

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2. Individual counts for Alterna [ 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...

0.47 0.44 0.53 8 513 7 0 7 0 10
2LDL_A - 1.00 1.00 1.00 9 131 1 0 0 1 0
2LK3_A - 1.00 1.00 1.00 9 91 0 0 0 0 0
3J16_L

tRNA links to Rfam database...

0.76 0.76 0.76 16 1138 5 3 2 0 5
3SN2_B

IRE_II links to Rfam database...

0.91 0.83 1.00 10 144 0 0 0 0 2
3UZL_B

tRNA links to Rfam database...

0.68 0.75 0.63 12 1274 13 4 3 6 4

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Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP 60
Total TN 3264
Total FP 56
Total FP CONTRA 19
Total FP INCONS 31
Total FP COMP 6
Total FN 25
Total Scores
MCC 0.610
Average MCC ± 95% Confidence Intervals 0.721 ± 0.307
Sensitivity 0.706
Positive Predictive Value 0.545
Nr of predictions 6

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2. Individual counts for NanoFolder [ 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...

0.54 0.61 0.50 11 506 11 1 10 0 7
2LDL_A - 1.00 1.00 1.00 9 131 1 0 0 1 0
2LK3_A - 1.00 1.00 1.00 9 91 0 0 0 0 0
3J16_L

tRNA links to Rfam database...

0.43 0.52 0.37 11 1129 19 8 11 0 10
3SN2_B

IRE_II links to Rfam database...

0.95 0.92 1.00 11 143 0 0 0 0 1
3UZL_B

tRNA links to Rfam database...

0.41 0.56 0.31 9 1264 25 10 10 5 7

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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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