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 ContextFold - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of TurboFold(seed) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for ContextFold & TurboFold(seed) [.zip] - may take several seconds...

Overview

Metric	ContextFold		TurboFold(seed)
MCC	0.576	>	0.460
Average MCC ± 95% Confidence Intervals	0.566 ± 0.210	>	0.454 ± 0.321
Sensitivity	0.449	>	0.380
Positive Predictive Value	0.743	>	0.563
Total TP	84	>	71
Total TN	27320	>	27307
Total FP	43	<	65
Total FP CONTRA	2	<	7
Total FP INCONS	27	<	48
Total FP COMP	14	>	10
Total FN	103	<	116
P-value	0.0

Performance plots

Performance of ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

Total Base Pair Counts
Total TP	84
Total TN	27320
Total FP	43
Total FP CONTRA	2
Total FP INCONS	27
Total FP COMP	14
Total FN	103

Total Scores
MCC	0.576
Average MCC ± 95% Confidence Intervals	0.566 ± 0.210
Sensitivity	0.449
Positive Predictive Value	0.743
Nr of predictions	6

2. Individual counts for ContextFold [ 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...	0.55	0.50	0.63	10	1524	6	0	6	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.15	0.28	5	11763	26	0	13	13	28
4A1C_3	5S_rRNA links to Rfam database...	0.78	0.63	0.97	34	7105	1	0	1	0	20
4AOB_A	SAM links to Rfam database...	0.52	0.40	0.68	17	4346	9	1	7	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Performance of TurboFold(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for TurboFold(seed)

Total Base Pair Counts
Total TP	71
Total TN	27307
Total FP	65
Total FP CONTRA	7
Total FP INCONS	48
Total FP COMP	10
Total FN	116

Total Scores
MCC	0.460
Average MCC ± 95% Confidence Intervals	0.454 ± 0.321
Sensitivity	0.380
Positive Predictive Value	0.563
Nr of predictions	6

2. Individual counts for TurboFold(seed) [ 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	1525	15	2	13	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	37	3	25	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	0	6	0	23
4AOB_A	SAM links to Rfam database...	0.56	0.40	0.77	17	4349	6	1	4	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
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.