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 RNASampler(seed) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	TurboFold(20)		RNASampler(seed)
MCC	0.582	>	0.581
Average MCC ± 95% Confidence Intervals	0.613 ± 0.512	>	0.594 ± 0.321
Sensitivity	0.488	>	0.426
Positive Predictive Value	0.700	<	0.797
Total TP	63	>	55
Total TN	18808	<	18829
Total FP	36	>	22
Total FP CONTRA	1	>	0
Total FP INCONS	26	>	14
Total FP COMP	9	>	8
Total FN	66	<	74
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	63
Total TN	18808
Total FP	36
Total FP CONTRA	1
Total FP INCONS	26
Total FP COMP	9
Total FN	66

Total Scores
MCC	0.582
Average MCC ± 95% Confidence Intervals	0.613 ± 0.512
Sensitivity	0.488
Positive Predictive Value	0.700
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
3SD1_A	THF links to Rfam database...	0.59	0.48	0.74	20	3889	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	28	0	19	9	28

Performance of RNASampler(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for RNASampler(seed)

Total Base Pair Counts
Total TP	55
Total TN	18829
Total FP	22
Total FP CONTRA	0
Total FP INCONS	14
Total FP COMP	8
Total FN	74

Total Scores
MCC	0.581
Average MCC ± 95% Confidence Intervals	0.594 ± 0.321
Sensitivity	0.426
Positive Predictive Value	0.797
Nr of predictions	4

2. Individual counts for RNASampler(seed) [ 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...	0.71	0.55	0.92	11	978	1	0	1	0	9
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.60	0.38	0.94	16	3899	1	0	1	0	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.31	0.24	0.40	8	11761	20	0	12	8	25

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