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 NanoFolder - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of RDfolder - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for NanoFolder & RDfolder [.zip] - may take several seconds...

Overview

Metric	NanoFolder		RDfolder
MCC	0.561	>	0.477
Average MCC ± 95% Confidence Intervals	0.698 ± 0.237	>	0.599 ± 0.332
Sensitivity	0.542	>	0.392
Positive Predictive Value	0.593	<	0.594
Total TP	83	>	60
Total TN	11136	<	11175
Total FP	60	>	42
Total FP CONTRA	4	>	3
Total FP INCONS	53	>	38
Total FP COMP	3	>	1
Total FN	70	<	93
P-value	0.0

Performance plots

Performance of NanoFolder - scored higher in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	83
Total TN	11136
Total FP	60
Total FP CONTRA	4
Total FP INCONS	53
Total FP COMP	3
Total FN	70

Total Scores
MCC	0.561
Average MCC ± 95% Confidence Intervals	0.698 ± 0.237
Sensitivity	0.542
Positive Predictive Value	0.593
Nr of predictions	8

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.52	0.55	0.50	11	1518	11	0	11	0	9
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
3J16_L	tRNA links to Rfam database...	0.36	0.37	0.37	11	2745	19	3	16	0	19
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.33	0.29	0.39	12	4340	20	1	18	1	30
4ENC_A	crcB links to Rfam database...	0.57	0.58	0.58	11	1307	9	0	8	1	8

Performance of RDfolder - scored lower in this pairwise comparison

1. Total counts & total scores for RDfolder

Total Base Pair Counts
Total TP	60
Total TN	11175
Total FP	42
Total FP CONTRA	3
Total FP INCONS	38
Total FP COMP	1
Total FN	93

Total Scores
MCC	0.477
Average MCC ± 95% Confidence Intervals	0.599 ± 0.332
Sensitivity	0.392
Positive Predictive Value	0.594
Nr of predictions	8

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1526	14	2	12	0	20
2LDL_A	-	0.90	0.82	1.00	9	342	0	0	0	0	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
3J16_L	tRNA links to Rfam database...	0.22	0.17	0.31	5	2759	11	0	11	0	25
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	0	4	0	13

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