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 PETfold_pre2.0(20) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	PETfold_pre2.0(seed)		PETfold_pre2.0(20)
MCC	0.678	>	0.625
Average MCC ± 95% Confidence Intervals	0.625 ± 0.179	>	0.581 ± 0.300
Sensitivity	0.557	>	0.497
Positive Predictive Value	0.830	>	0.790
Total TP	93	>	83
Total TN	25781	<	25788
Total FP	26	<	33
Total FP CONTRA	2	>	0
Total FP INCONS	17	<	22
Total FP COMP	7	<	11
Total FN	74	<	84
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 PETfold_pre2.0(20) - scored lower 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

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