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(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

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

Total counts & total scores
Individual counts

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

Overview

Metric	PETfold_pre2.0(20)		MXScarna(seed)
MCC	0.625	>	0.593
Average MCC ± 95% Confidence Intervals	0.581 ± 0.300	>	0.533 ± 0.207
Sensitivity	0.497	>	0.467
Positive Predictive Value	0.790	>	0.757
Total TP	83	>	78
Total TN	25788	<	25790
Total FP	33	<	38
Total FP CONTRA	0	<	3
Total FP INCONS	22	=	22
Total FP COMP	11	<	13
Total FN	84	<	89
P-value	0.0

Performance plots

Performance of PETfold_pre2.0(20) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(20)

Total Base Pair Counts
Total TP	83
Total TN	25788
Total FP	33
Total FP CONTRA	0
Total FP INCONS	22
Total FP COMP	11
Total FN	84

Total Scores
MCC	0.625
Average MCC ± 95% Confidence Intervals	0.581 ± 0.300
Sensitivity	0.497
Positive Predictive Value	0.790
Nr of predictions	5

2. Individual counts for PETfold_pre2.0(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...	0.19	0.15	0.25	5	11761	25	0	15	10	28
4A1C_3	5S_rRNA links to Rfam database...	0.82	0.69	0.97	37	7102	1	0	1	0	17
4AOB_A	SAM links to Rfam database...	0.74	0.60	0.93	25	4344	3	0	2	1	17
4ENB_A	crcB links to Rfam database...	0.61	0.42	0.89	8	1266	1	0	1	0	11
4ENC_A	crcB links to Rfam database...	0.55	0.42	0.73	8	1315	3	0	3	0	11

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

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

Total Base Pair Counts
Total TP	78
Total TN	25790
Total FP	38
Total FP CONTRA	3
Total FP INCONS	22
Total FP COMP	13
Total FN	89

Total Scores
MCC	0.593
Average MCC ± 95% Confidence Intervals	0.533 ± 0.207
Sensitivity	0.467
Positive Predictive Value	0.757
Nr of predictions	5

2. Individual counts for MXScarna(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...	0.35	0.24	0.50	8	11765	20	1	7	12	25
4A1C_3	5S_rRNA links to Rfam database...	0.75	0.65	0.88	35	7100	5	1	4	0	19
4AOB_A	SAM links to Rfam database...	0.66	0.55	0.79	23	4342	7	0	6	1	19
4ENB_A	crcB links to Rfam database...	0.48	0.32	0.75	6	1267	2	0	2	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	1	3	0	13

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