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

Home

RNA 2D Atlas

Help

FAQ

Table of contents:

Overview

Performance Plots

Performance of RDfolder - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

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

Total counts & total scores
Individual counts

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

Overview

Metric	RDfolder		PPfold(seed)
MCC	0.342	>	0.138
Average MCC ± 95% Confidence Intervals	0.332 ± 0.190	>	0.059 ± 0.139
Sensitivity	0.253	>	0.026
Positive Predictive Value	0.476	<	0.750
Total TP	59	>	6
Total TN	20293	<	20409
Total FP	68	>	2
Total FP CONTRA	5	>	0
Total FP INCONS	60	>	2
Total FP COMP	3	>	0
Total FN	174	<	227
P-value	0.0

Performance plots

Performance of RDfolder - scored higher in this pairwise comparison

1. Total counts & total scores for RDfolder

Total Base Pair Counts
Total TP	59
Total TN	20293
Total FP	68
Total FP CONTRA	5
Total FP INCONS	60
Total FP COMP	3
Total FN	174

Total Scores
MCC	0.342
Average MCC ± 95% Confidence Intervals	0.332 ± 0.190
Sensitivity	0.253
Positive Predictive Value	0.476
Nr of predictions	8

2. Individual counts for RDfolder [ 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	1526	14	2	12	0	20
3AMU_B	tRNA links to Rfam database...	0.18	0.15	0.22	4	2985	16	2	12	2	23
3J16_L	tRNA links to Rfam database...	0.22	0.17	0.31	5	2759	11	0	11	0	25
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.30	0.17	0.54	7	3903	6	0	6	0	35
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1265	4	0	4	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	0	4	0	13

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

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

Total Base Pair Counts
Total TP	6
Total TN	20409
Total FP	2
Total FP CONTRA	0
Total FP INCONS	2
Total FP COMP	0
Total FN	227

Total Scores
MCC	0.138
Average MCC ± 95% Confidence Intervals	0.059 ± 0.139
Sensitivity	0.026
Positive Predictive Value	0.750
Nr of predictions	8

2. Individual counts for PPfold(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...	0.47	0.30	0.75	6	1532	2	0	2	0	14
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3003	0	0	0	0	27
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	2775	0	0	0	0	30
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2211	0	0	0	0	34
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	42
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	42
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19

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