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 PknotsRG - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of Multilign(20) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	PknotsRG		Multilign(20)
MCC	0.592	>	0.521
Average MCC ± 95% Confidence Intervals	0.648 ± 0.185	>	0.526 ± 0.210
Sensitivity	0.521	>	0.428
Positive Predictive Value	0.678	>	0.643
Total TP	173	>	142
Total TN	40909	<	40943
Total FP	94	>	86
Total FP CONTRA	11	>	8
Total FP INCONS	71	=	71
Total FP COMP	12	>	7
Total FN	159	<	190
P-value	1.26497248087e-08

Performance plots

Performance of PknotsRG - scored higher in this pairwise comparison

1. Total counts & total scores for PknotsRG

Total Base Pair Counts
Total TP	173
Total TN	40909
Total FP	94
Total FP CONTRA	11
Total FP INCONS	71
Total FP COMP	12
Total FN	159

Total Scores
MCC	0.592
Average MCC ± 95% Confidence Intervals	0.648 ± 0.185
Sensitivity	0.521
Positive Predictive Value	0.678
Nr of predictions	10

2. Individual counts for PknotsRG [ 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...	0.97	0.95	1.00	19	971	0	0	0	0	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.34	0.31	0.39	13	5118	20	1	19	0	29
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
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...	0.61	0.50	0.75	21	3888	7	1	6	0	21
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.13	5	11742	43	5	29	9	28
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

Performance of Multilign(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	142
Total TN	40943
Total FP	86
Total FP CONTRA	8
Total FP INCONS	71
Total FP COMP	7
Total FN	190

Total Scores
MCC	0.521
Average MCC ± 95% Confidence Intervals	0.526 ± 0.210
Sensitivity	0.428
Positive Predictive Value	0.643
Nr of predictions	10

2. Individual counts for Multilign(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...	0.97	0.95	1.00	19	971	0	0	0	0	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5139	12	1	11	0	42
3AMU_B	tRNA links to Rfam database...	0.63	0.56	0.71	15	2982	8	0	6	2	12
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.57	0.48	0.69	20	3887	9	1	8	0	22
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.84	32	7102	6	0	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11747	33	3	26	4	28
4AOB_A	SAM links to Rfam database...	0.49	0.38	0.64	16	4346	10	1	8	1	26
4ENB_A	crcB links to Rfam database...	0.34	0.26	0.45	5	1264	6	1	5	0	14
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

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