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 RNASLOpt - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

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

Total counts & total scores
Individual counts

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

Overview

Metric	RNASLOpt		Carnac(seed)
MCC	0.467	>	0.146
Average MCC ± 95% Confidence Intervals	0.506 ± 0.235	>	0.074 ± 0.191
Sensitivity	0.380	>	0.021
Positive Predictive Value	0.582	<	1.000
Total TP	71	>	4
Total TN	27311	<	27429
Total FP	57	>	0
Total FP CONTRA	11	>	0
Total FP INCONS	40	>	0
Total FP COMP	6	>	0
Total FN	116	<	183
P-value	0.0

Performance plots

Performance of RNASLOpt - scored higher in this pairwise comparison

1. Total counts & total scores for RNASLOpt

Total Base Pair Counts
Total TP	71
Total TN	27311
Total FP	57
Total FP CONTRA	11
Total FP INCONS	40
Total FP COMP	6
Total FN	116

Total Scores
MCC	0.467
Average MCC ± 95% Confidence Intervals	0.506 ± 0.235
Sensitivity	0.380
Positive Predictive Value	0.582
Nr of predictions	6

2. Individual counts for RNASLOpt [ 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	0.35	0.64	7	1529	4	0	4	0	13
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4AOB_A	SAM links to Rfam database...	0.26	0.19	0.38	8	4350	13	2	11	0	34
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

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

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

Total Base Pair Counts
Total TP	4
Total TN	27429
Total FP	0
Total FP CONTRA	0
Total FP INCONS	0
Total FP COMP	0
Total FN	183

Total Scores
MCC	0.146
Average MCC ± 95% Confidence Intervals	0.074 ± 0.191
Sensitivity	0.021
Positive Predictive Value	1.000
Nr of predictions	6

2. Individual counts for Carnac(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...	0.44	0.20	1.00	4	1536	0	0	0	0	16
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11781	0	0	0	0	33
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
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.