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(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of ProbKnot - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	PETfold_pre2.0(20)		ProbKnot
MCC	0.625	>	0.488
Average MCC ± 95% Confidence Intervals	0.581 ± 0.300	>	0.507 ± 0.305
Sensitivity	0.497	>	0.443
Positive Predictive Value	0.790	>	0.544
Total TP	83	>	74
Total TN	25788	>	25757
Total FP	33	<	75
Total FP CONTRA	0	<	12
Total FP INCONS	22	<	50
Total FP COMP	11	<	13
Total FN	84	<	93
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 ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	74
Total TN	25757
Total FP	75
Total FP CONTRA	12
Total FP INCONS	50
Total FP COMP	13
Total FN	93

Total Scores
MCC	0.488
Average MCC ± 95% Confidence Intervals	0.507 ± 0.305
Sensitivity	0.443
Positive Predictive Value	0.544
Nr of predictions	5

2. Individual counts for ProbKnot [ 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...	0.13	0.15	0.12	5	11738	49	7	31	11	28
4A1C_3	5S_rRNA links to Rfam database...	0.73	0.61	0.87	33	7102	6	1	4	1	21
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENB_A	crcB links to Rfam database...	0.73	0.58	0.92	11	1263	1	1	0	0	8
4ENC_A	crcB links to Rfam database...	0.45	0.42	0.50	8	1310	8	1	7	0	11

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