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 NanoFolder - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	TurboFold(seed)		NanoFolder
MCC	0.439	>	0.341
Average MCC ± 95% Confidence Intervals	0.407 ± 0.394	>	0.379 ± 0.289
Sensitivity	0.369	>	0.351
Positive Predictive Value	0.530	>	0.339
Total TP	62	>	59
Total TN	26041	>	25984
Total FP	65	<	125
Total FP CONTRA	7	<	15
Total FP INCONS	48	<	100
Total FP COMP	10	=	10
Total FN	106	<	109
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	62
Total TN	26041
Total FP	65
Total FP CONTRA	7
Total FP INCONS	48
Total FP COMP	10
Total FN	106

Total Scores
MCC	0.439
Average MCC ± 95% Confidence Intervals	0.407 ± 0.394
Sensitivity	0.369
Positive Predictive Value	0.530
Nr of predictions	5

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
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	59
Total TN	25984
Total FP	125
Total FP CONTRA	15
Total FP INCONS	100
Total FP COMP	10
Total FN	109

Total Scores
MCC	0.341
Average MCC ± 95% Confidence Intervals	0.379 ± 0.289
Sensitivity	0.351
Positive Predictive Value	0.339
Nr of predictions	5

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
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11728	61	12	41	8	33
4A1C_3	5S_rRNA links to Rfam database...	0.48	0.46	0.51	25	7091	24	2	22	0	29
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

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