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 RNASampler(seed) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of ProbKnot - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	RNASampler(seed)		ProbKnot
MCC	0.568	>	0.543
Average MCC ± 95% Confidence Intervals	0.557 ± 0.244	<	0.581 ± 0.334
Sensitivity	0.429	<	0.528
Positive Predictive Value	0.758	>	0.564
Total TP	100	<	123
Total TN	36934	>	36848
Total FP	44	<	118
Total FP CONTRA	2	<	16
Total FP INCONS	30	<	79
Total FP COMP	12	<	23
Total FN	133	>	110
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	100
Total TN	36934
Total FP	44
Total FP CONTRA	2
Total FP INCONS	30
Total FP COMP	12
Total FN	133

Total Scores
MCC	0.568
Average MCC ± 95% Confidence Intervals	0.557 ± 0.244
Sensitivity	0.429
Positive Predictive Value	0.758
Nr of predictions	8

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_B	Gammaretro_CES links to Rfam database...	0.82	0.68	1.00	17	2128	0	0	0	0	8
2L1F_A	Gammaretro_CES links to Rfam database...	0.81	0.67	1.00	16	2064	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
4A1C_2	5_8S_rRNA links to Rfam database...	0.31	0.24	0.40	8	11761	20	0	12	8	25

Performance of ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	123
Total TN	36848
Total FP	118
Total FP CONTRA	16
Total FP INCONS	79
Total FP COMP	23
Total FN	110

Total Scores
MCC	0.543
Average MCC ± 95% Confidence Intervals	0.581 ± 0.334
Sensitivity	0.528
Positive Predictive Value	0.564
Nr of predictions	8

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
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...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
3O58_3	5_8S_rRNA links to Rfam database...	0.31	0.34	0.29	12	12362	41	4	25	12	23
3RKF_A	Purine links to Rfam database...	0.73	0.59	0.91	20	2189	2	1	1	0	14
3SD1_A	THF links to Rfam database...	0.55	0.48	0.65	20	3885	11	2	9	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.12	5	11738	49	7	31	11	28

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