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 PETfold_pre2.0(seed) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of Murlet(seed) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for PETfold_pre2.0(seed) & Murlet(seed) [.zip] - may take several seconds...

Overview

Metric	PETfold_pre2.0(seed)		Murlet(seed)
MCC	0.575	>	0.425
Average MCC ± 95% Confidence Intervals	0.540 ± 0.149	>	0.429 ± 0.310
Sensitivity	0.459	>	0.248
Positive Predictive Value	0.726	<	0.733
Total TP	61	>	33
Total TN	20209	<	20248
Total FP	30	>	13
Total FP CONTRA	2	>	0
Total FP INCONS	21	>	12
Total FP COMP	7	>	1
Total FN	72	<	100
P-value	0.0

Performance plots

Performance of PETfold_pre2.0(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(seed)

Total Base Pair Counts
Total TP	61
Total TN	20209
Total FP	30
Total FP CONTRA	2
Total FP INCONS	21
Total FP COMP	7
Total FN	72

Total Scores
MCC	0.575
Average MCC ± 95% Confidence Intervals	0.540 ± 0.149
Sensitivity	0.459
Positive Predictive Value	0.726
Nr of predictions	5

2. Individual counts for PETfold_pre2.0(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...	0.40	0.30	0.55	6	1529	5	0	5	0	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.57	0.45	0.71	15	11760	12	0	6	6	18
4AOB_A	SAM links to Rfam database...	0.72	0.57	0.92	24	4345	3	0	2	1	18
4ENB_A	crcB links to Rfam database...	0.50	0.42	0.62	8	1262	5	1	4	0	11
4ENC_A	crcB links to Rfam database...	0.50	0.42	0.62	8	1313	5	1	4	0	11

Performance of Murlet(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	33
Total TN	20248
Total FP	13
Total FP CONTRA	0
Total FP INCONS	12
Total FP COMP	1
Total FN	100

Total Scores
MCC	0.425
Average MCC ± 95% Confidence Intervals	0.429 ± 0.310
Sensitivity	0.248
Positive Predictive Value	0.733
Nr of predictions	5

2. Individual counts for Murlet(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	1528	12	0	12	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	11774	0	0	0	0	26
4AOB_A	SAM links to Rfam database...	0.58	0.33	1.00	14	4357	1	0	0	1	28
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13

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