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 Carnac(20) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	RNASampler(seed)		Carnac(20)
MCC	0.582	>	0.574
Average MCC ± 95% Confidence Intervals	0.619 ± 0.185	>	0.521 ± 0.221
Sensitivity	0.444	>	0.343
Positive Predictive Value	0.768	<	0.965
Total TP	106	>	82
Total TN	46161	<	46214
Total FP	47	>	6
Total FP CONTRA	4	>	0
Total FP INCONS	28	>	3
Total FP COMP	15	>	3
Total FN	133	<	157
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	106
Total TN	46161
Total FP	47
Total FP CONTRA	4
Total FP INCONS	28
Total FP COMP	15
Total FN	133

Total Scores
MCC	0.582
Average MCC ± 95% Confidence Intervals	0.619 ± 0.185
Sensitivity	0.444
Positive Predictive Value	0.768
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
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.71	0.55	0.92	11	978	1	0	1	0	9
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.30	0.50	10	12226	13	2	8	3	23
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 Carnac(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	82
Total TN	46214
Total FP	6
Total FP CONTRA	0
Total FP INCONS	3
Total FP COMP	3
Total FN	157

Total Scores
MCC	0.574
Average MCC ± 95% Confidence Intervals	0.521 ± 0.221
Sensitivity	0.343
Positive Predictive Value	0.965
Nr of predictions	8

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.73	0.55	1.00	6	400	0	0	0	0	5
2L94_A	HIV_FE links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	20
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	12239	2	0	0	2	26
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.26	1.00	9	12394	0	0	0	0	26
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...	0.33	0.15	0.71	5	11774	3	0	2	1	28

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