CompaRNA - on-line benchmarks of RNA structure prediction methods

CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Table of contents:

Overview

Performance Plots

Performance of TurboFold(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of Afold - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for TurboFold(20) & Afold [.zip] - may take several seconds...

Overview

Metric	TurboFold(20)		Afold
MCC	0.593	>	0.564
Average MCC ± 95% Confidence Intervals	0.637 ± 0.514	<	0.638 ± 0.563
Sensitivity	0.491	<	0.519
Positive Predictive Value	0.722	>	0.618
Total TP	52	<	55
Total TN	16185	>	16168
Total FP	29	<	46
Total FP CONTRA	0	<	6
Total FP INCONS	20	<	28
Total FP COMP	9	<	12
Total FN	54	>	51
P-value	0.0

Performance plots

Performance of TurboFold(20) - scored higher in this pairwise comparison

1. Total counts & total scores for TurboFold(20)

Total Base Pair Counts
Total TP	52
Total TN	16185
Total FP	29
Total FP CONTRA	0
Total FP INCONS	20
Total FP COMP	9
Total FN	54

Total Scores
MCC	0.593
Average MCC ± 95% Confidence Intervals	0.637 ± 0.514
Sensitivity	0.491
Positive Predictive Value	0.722
Nr of predictions	4

2. Individual counts for TurboFold(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.92	0.90	0.95	18	971	1	0	1	0	2
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	28	0	19	9	28
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10

Performance of Afold - scored lower in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP	55
Total TN	16168
Total FP	46
Total FP CONTRA	6
Total FP INCONS	28
Total FP COMP	12
Total FN	51

Total Scores
MCC	0.564
Average MCC ± 95% Confidence Intervals	0.638 ± 0.563
Sensitivity	0.519
Positive Predictive Value	0.618
Nr of predictions	4

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
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
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

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