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(seed) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of CRWrnafold - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	RNAalifold(seed)		CRWrnafold
MCC	0.500	>	0.419
Average MCC ± 95% Confidence Intervals	0.467 ± 0.269	>	0.438 ± 0.318
Sensitivity	0.320	<	0.377
Positive Predictive Value	0.789	>	0.475
Total TP	56	<	66
Total TN	24138	>	24070
Total FP	18	<	83
Total FP CONTRA	1	<	12
Total FP INCONS	14	<	61
Total FP COMP	3	<	10
Total FN	119	>	109
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	56
Total TN	24138
Total FP	18
Total FP CONTRA	1
Total FP INCONS	14
Total FP COMP	3
Total FN	119

Total Scores
MCC	0.500
Average MCC ± 95% Confidence Intervals	0.467 ± 0.269
Sensitivity	0.320
Positive Predictive Value	0.789
Nr of predictions	6

2. Individual counts for RNAalifold(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
3SD1_A	THF links to Rfam database...	0.58	0.40	0.85	17	3896	3	1	2	0	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.39	0.15	1.00	5	11776	2	0	0	2	28
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
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

Performance of CRWrnafold - scored lower in this pairwise comparison

1. Total counts & total scores for CRWrnafold

Total Base Pair Counts
Total TP	66
Total TN	24070
Total FP	83
Total FP CONTRA	12
Total FP INCONS	61
Total FP COMP	10
Total FN	109

Total Scores
MCC	0.419
Average MCC ± 95% Confidence Intervals	0.438 ± 0.318
Sensitivity	0.377
Positive Predictive Value	0.475
Nr of predictions	6

2. Individual counts for CRWrnafold [ 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
3SD1_A	THF links to Rfam database...	0.52	0.45	0.61	19	3885	12	2	10	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.13	5	11741	44	4	31	9	28
4AOB_A	SAM links to Rfam database...	0.59	0.48	0.74	20	4344	8	2	5	1	22
4ENB_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1313	2	1	1	0	8

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