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

Overview

Metric	RNAalifold(20)		NanoFolder
MCC	0.565	>	0.316
Average MCC ± 95% Confidence Intervals	0.549 ± 0.424	>	0.345 ± 0.403
Sensitivity	0.432	>	0.324
Positive Predictive Value	0.744	>	0.316
Total TP	64	>	48
Total TN	24532	>	24466
Total FP	25	<	114
Total FP CONTRA	2	<	15
Total FP INCONS	20	<	89
Total FP COMP	3	<	10
Total FN	84	<	100
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	64
Total TN	24532
Total FP	25
Total FP CONTRA	2
Total FP INCONS	20
Total FP COMP	3
Total FN	84

Total Scores
MCC	0.565
Average MCC ± 95% Confidence Intervals	0.549 ± 0.424
Sensitivity	0.432
Positive Predictive Value	0.744
Nr of predictions	4

2. Individual counts for RNAalifold(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...	0.17	0.15	0.19	5	11755	23	2	19	2	28
4A1C_3	5S_rRNA links to Rfam database...	0.74	0.57	0.97	31	7108	1	0	1	0	23
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13

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.