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 Murlet(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of Alterna - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	Murlet(20)		Alterna
MCC	0.658	>	0.571
Average MCC ± 95% Confidence Intervals	0.649 ± 0.073	>	0.603 ± 0.155
Sensitivity	0.510	>	0.504
Positive Predictive Value	0.856	>	0.656
Total TP	185	>	183
Total TN	35548	>	35485
Total FP	38	<	118
Total FP CONTRA	7	<	11
Total FP INCONS	24	<	85
Total FP COMP	7	<	22
Total FN	178	<	180
P-value	1.66062906821e-08

Performance plots

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

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

Total Base Pair Counts
Total TP	185
Total TN	35548
Total FP	38
Total FP CONTRA	7
Total FP INCONS	24
Total FP COMP	7
Total FN	178

Total Scores
MCC	0.658
Average MCC ± 95% Confidence Intervals	0.649 ± 0.073
Sensitivity	0.510
Positive Predictive Value	0.856
Nr of predictions	13

2. Individual counts for Murlet(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...	0.67	0.45	1.00	5	401	0	0	0	0	6
2L94_A	HIV_FE links to Rfam database...	0.53	0.50	0.59	10	973	7	0	7	0	10
2WRQ_Y	tRNA links to Rfam database...	0.41	0.41	0.41	7	2833	12	6	4	2	10
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	4	4556	3	0	0	3	16
2XQD_Y	tRNA links to Rfam database...	0.80	0.70	0.90	19	2829	2	0	2	0	8
3A2K_C	tRNA links to Rfam database...	0.78	0.68	0.90	19	2905	2	0	2	0	9
3AMU_B	tRNA links to Rfam database...	0.77	0.67	0.90	18	2983	3	0	2	1	9
3GX2_A	SAM links to Rfam database...	0.61	0.38	1.00	15	4356	1	0	0	1	25
3IVN_B	Purine links to Rfam database...	0.69	0.48	1.00	15	2331	0	0	0	0	16
3JYV_7	tRNA links to Rfam database...	0.67	0.53	0.85	17	2830	3	0	3	0	15
3LA5_A	Purine links to Rfam database...	0.68	0.47	1.00	16	2469	0	0	0	0	18
3RKF_A	Purine links to Rfam database...	0.68	0.47	1.00	16	2195	0	0	0	0	18
3SD1_A	THF links to Rfam database...	0.68	0.57	0.83	24	3887	5	1	4	0	18

Performance of Alterna - scored lower in this pairwise comparison

1. Total counts & total scores for Alterna

Total Base Pair Counts
Total TP	183
Total TN	35485
Total FP	118
Total FP CONTRA	11
Total FP INCONS	85
Total FP COMP	22
Total FN	180

Total Scores
MCC	0.571
Average MCC ± 95% Confidence Intervals	0.603 ± 0.155
Sensitivity	0.504
Positive Predictive Value	0.656
Nr of predictions	13

2. Individual counts for Alterna [ 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...	0.97	0.95	1.00	19	971	0	0	0	0	1
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.45	0.45	0.45	9	4540	25	0	11	14	11
2XQD_Y	tRNA links to Rfam database...	0.67	0.59	0.76	16	2829	5	0	5	0	11
3A2K_C	tRNA links to Rfam database...	0.44	0.43	0.46	12	2900	14	2	12	0	16
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3GX2_A	SAM links to Rfam database...	0.47	0.40	0.57	16	4343	13	1	11	1	24
3IVN_B	Purine links to Rfam database...	0.74	0.61	0.90	19	2325	2	1	1	0	12
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2828	22	0	22	0	32
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3RKF_A	Purine links to Rfam database...	0.69	0.56	0.86	19	2189	3	1	2	0	15
3SD1_A	THF links to Rfam database...	0.46	0.38	0.57	16	3888	12	1	11	0	26

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