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 RNAshapes - 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 RNAshapes & Multilign(20) [.zip] - may take several seconds...

Overview

Metric	RNAshapes		Multilign(20)
MCC	0.633	>	0.521
Average MCC ± 95% Confidence Intervals	0.635 ± 0.182	>	0.526 ± 0.210
Sensitivity	0.548	>	0.428
Positive Predictive Value	0.737	>	0.643
Total TP	182	>	142
Total TN	40917	<	40943
Total FP	79	<	86
Total FP CONTRA	11	>	8
Total FP INCONS	54	<	71
Total FP COMP	14	>	7
Total FN	150	<	190
P-value	1.32883086441e-08

Performance plots

Performance of RNAshapes - scored higher in this pairwise comparison

1. Total counts & total scores for RNAshapes

Total Base Pair Counts
Total TP	182
Total TN	40917
Total FP	79
Total FP CONTRA	11
Total FP INCONS	54
Total FP COMP	14
Total FN	150

Total Scores
MCC	0.633
Average MCC ± 95% Confidence Intervals	0.635 ± 0.182
Sensitivity	0.548
Positive Predictive Value	0.737
Nr of predictions	10

2. Individual counts for RNAshapes [ 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...	0.93	0.86	1.00	36	5115	0	0	0	0	6
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...	0.64	0.52	0.79	22	3888	6	1	5	0	20
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.57	0.82	31	7102	7	1	6	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11746	41	5	25	11	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...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1314	7	1	6	0	14

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.