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

Overview

Metric	Multilign(20)		NanoFolder
MCC	0.490	>	0.316
Average MCC ± 95% Confidence Intervals	0.498 ± 0.399	>	0.345 ± 0.403
Sensitivity	0.419	>	0.324
Positive Predictive Value	0.579	>	0.316
Total TP	62	>	48
Total TN	24511	>	24466
Total FP	50	<	114
Total FP CONTRA	5	<	15
Total FP INCONS	40	<	89
Total FP COMP	5	<	10
Total FN	86	<	100
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	62
Total TN	24511
Total FP	50
Total FP CONTRA	5
Total FP INCONS	40
Total FP COMP	5
Total FN	86

Total Scores
MCC	0.490
Average MCC ± 95% Confidence Intervals	0.498 ± 0.399
Sensitivity	0.419
Positive Predictive Value	0.579
Nr of predictions	4

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.84	32	7102	6	0	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11747	33	3	26	4	28
4AOB_A	SAM links to Rfam database...	0.49	0.38	0.64	16	4346	10	1	8	1	26
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	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_3	5S_rRNA links to Rfam database...	0.48	0.46	0.51	25	7091	24	2	22	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11728	61	12	41	8	33
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.