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 Cylofold - 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 Cylofold & RNASampler(seed) [.zip] - may take several seconds...

Overview

Metric	Cylofold		RNASampler(seed)
MCC	0.702	>	0.613
Average MCC ± 95% Confidence Intervals	0.736 ± 0.205	>	0.593 ± 0.274
Sensitivity	0.620	>	0.460
Positive Predictive Value	0.800	<	0.821
Total TP	124	>	92
Total TN	25130	<	25173
Total FP	40	>	24
Total FP CONTRA	5	>	2
Total FP INCONS	26	>	18
Total FP COMP	9	>	4
Total FN	76	<	108
P-value	0.0

Performance plots

Performance of Cylofold - scored higher in this pairwise comparison

1. Total counts & total scores for Cylofold

Total Base Pair Counts
Total TP	124
Total TN	25130
Total FP	40
Total FP CONTRA	5
Total FP INCONS	26
Total FP COMP	9
Total FN	76

Total Scores
MCC	0.702
Average MCC ± 95% Confidence Intervals	0.736 ± 0.205
Sensitivity	0.620
Positive Predictive Value	0.800
Nr of predictions	7

2. Individual counts for Cylofold [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L1F_A	Gammaretro_CES links to Rfam database...	0.91	0.83	1.00	20	2060	0	0	0	0	4
2L1F_B	Gammaretro_CES links to Rfam database...	0.92	0.84	1.00	21	2124	0	0	0	0	4
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
3O58_3	5_8S_rRNA links to Rfam database...	0.36	0.34	0.38	12	12371	29	5	15	9	23
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...	0.62	0.50	0.78	21	3889	6	0	6	0	21

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

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

Total Base Pair Counts
Total TP	92
Total TN	25173
Total FP	24
Total FP CONTRA	2
Total FP INCONS	18
Total FP COMP	4
Total FN	108

Total Scores
MCC	0.613
Average MCC ± 95% Confidence Intervals	0.593 ± 0.274
Sensitivity	0.460
Positive Predictive Value	0.821
Nr of predictions	7

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
2L1F_A	Gammaretro_CES links to Rfam database...	0.81	0.67	1.00	16	2064	0	0	0	0	8
2L1F_B	Gammaretro_CES links to Rfam database...	0.82	0.68	1.00	17	2128	0	0	0	0	8
2L94_A	HIV_FE links to Rfam database...	0.71	0.55	0.92	11	978	1	0	1	0	9
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1530	10	0	10	0	20
3O58_3	5_8S_rRNA links to Rfam database...	0.45	0.34	0.60	12	12383	12	2	6	4	23
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

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