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 TurboFold(seed) - 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 TurboFold(seed) & RDfolder [.zip] - may take several seconds...

Overview

Metric	TurboFold(seed)		RDfolder
MCC	0.598	>	0.467
Average MCC ± 95% Confidence Intervals	0.594 ± 0.271	>	0.462 ± 0.297
Sensitivity	0.474	>	0.352
Positive Predictive Value	0.762	>	0.633
Total TP	93	>	69
Total TN	15507	<	15520
Total FP	30	<	41
Total FP CONTRA	5	>	3
Total FP INCONS	24	<	37
Total FP COMP	1	=	1
Total FN	103	<	127
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	93
Total TN	15507
Total FP	30
Total FP CONTRA	5
Total FP INCONS	24
Total FP COMP	1
Total FN	103

Total Scores
MCC	0.598
Average MCC ± 95% Confidence Intervals	0.594 ± 0.271
Sensitivity	0.474
Positive Predictive Value	0.762
Nr of predictions	7

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
2L94_A	HIV_FE links to Rfam database...	0.92	0.90	0.95	18	971	1	0	1	0	2
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
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...	0.59	0.48	0.74	20	3889	7	1	6	0	22
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

Performance of RDfolder - scored lower in this pairwise comparison

1. Total counts & total scores for RDfolder

Total Base Pair Counts
Total TP	69
Total TN	15520
Total FP	41
Total FP CONTRA	3
Total FP INCONS	37
Total FP COMP	1
Total FN	127

Total Scores
MCC	0.467
Average MCC ± 95% Confidence Intervals	0.462 ± 0.297
Sensitivity	0.352
Positive Predictive Value	0.633
Nr of predictions	7

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
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1526	14	2	12	0	20
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...	0.30	0.17	0.54	7	3903	6	0	6	0	35
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1265	4	0	4	0	13
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.