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 RNAalifold(20) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for PETfold_pre2.0(seed) & RNAalifold(20) [.zip] - may take several seconds...

Overview

Metric	PETfold_pre2.0(seed)		RNAalifold(20)
MCC	0.678	>	0.553
Average MCC ± 95% Confidence Intervals	0.625 ± 0.179	>	0.530 ± 0.291
Sensitivity	0.557	>	0.407
Positive Predictive Value	0.830	>	0.756
Total TP	93	>	68
Total TN	25781	<	25803
Total FP	26	>	25
Total FP CONTRA	2	=	2
Total FP INCONS	17	<	20
Total FP COMP	7	>	3
Total FN	74	<	99
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	93
Total TN	25781
Total FP	26
Total FP CONTRA	2
Total FP INCONS	17
Total FP COMP	7
Total FN	74

Total Scores
MCC	0.678
Average MCC ± 95% Confidence Intervals	0.625 ± 0.179
Sensitivity	0.557
Positive Predictive Value	0.830
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
4A1C_2	5_8S_rRNA links to Rfam database...	0.57	0.45	0.71	15	11760	12	0	6	6	18
4A1C_3	5S_rRNA links to Rfam database...	0.83	0.70	0.97	38	7101	1	0	1	0	16
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 RNAalifold(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	68
Total TN	25803
Total FP	25
Total FP CONTRA	2
Total FP INCONS	20
Total FP COMP	3
Total FN	99

Total Scores
MCC	0.553
Average MCC ± 95% Confidence Intervals	0.530 ± 0.291
Sensitivity	0.407
Positive Predictive Value	0.756
Nr of predictions	5

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
4ENB_A	crcB links to Rfam database...	0.46	0.21	1.00	4	1271	0	0	0	0	15
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.