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 Carnac(20) - 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 Carnac(20) & NanoFolder [.zip] - may take several seconds...

Overview

Metric	Carnac(20)		NanoFolder
MCC	0.506	>	0.316
Average MCC ± 95% Confidence Intervals	0.373 ± 0.454	>	0.345 ± 0.403
Sensitivity	0.318	<	0.324
Positive Predictive Value	0.810	>	0.316
Total TP	47	<	48
Total TN	24560	>	24466
Total FP	13	<	114
Total FP CONTRA	1	<	15
Total FP INCONS	10	<	89
Total FP COMP	2	<	10
Total FN	101	>	100
P-value	0.0

Performance plots

Performance of Carnac(20) - scored higher in this pairwise comparison

1. Total counts & total scores for Carnac(20)

Total Base Pair Counts
Total TP	47
Total TN	24560
Total FP	13
Total FP CONTRA	1
Total FP INCONS	10
Total FP COMP	2
Total FN	101

Total Scores
MCC	0.506
Average MCC ± 95% Confidence Intervals	0.373 ± 0.454
Sensitivity	0.318
Positive Predictive Value	0.810
Nr of predictions	4

2. Individual counts for Carnac(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.15	0.71	5	11774	3	0	2	1	28
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4AOB_A	SAM links to Rfam database...	0.49	0.33	0.74	14	4352	6	1	4	1	28
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	48
Total TN	24466
Total FP	114
Total FP CONTRA	15
Total FP INCONS	89
Total FP COMP	10
Total FN	100

Total Scores
MCC	0.316
Average MCC ± 95% Confidence Intervals	0.345 ± 0.403
Sensitivity	0.324
Positive Predictive Value	0.316
Nr of predictions	4

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
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.