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 TurboFold(seed) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of Mastr(20) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	TurboFold(seed)		Mastr(20)
MCC	0.595	>	0.572
Average MCC ± 95% Confidence Intervals	0.626 ± 0.187	>	0.522 ± 0.223
Sensitivity	0.490	>	0.399
Positive Predictive Value	0.729	<	0.827
Total TP	129	>	105
Total TN	32833	<	32883
Total FP	58	>	24
Total FP CONTRA	6	>	1
Total FP INCONS	42	>	21
Total FP COMP	10	>	2
Total FN	134	<	158
P-value	0.0

Performance plots

Performance of TurboFold(seed) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	129
Total TN	32833
Total FP	58
Total FP CONTRA	6
Total FP INCONS	42
Total FP COMP	10
Total FN	134

Total Scores
MCC	0.595
Average MCC ± 95% Confidence Intervals	0.626 ± 0.187
Sensitivity	0.490
Positive Predictive Value	0.729
Nr of predictions	8

2. Individual counts for TurboFold(seed) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.92	0.90	0.95	18	971	1	0	1	0	2
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...	0.59	0.48	0.74	20	3889	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	37	3	25	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	0	6	0	23
4AOB_A	SAM links to Rfam database...	0.56	0.40	0.77	17	4349	6	1	4	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Performance of Mastr(20) - scored lower in this pairwise comparison

1. Total counts & total scores for Mastr(20)

Total Base Pair Counts
Total TP	105
Total TN	32883
Total FP	24
Total FP CONTRA	1
Total FP INCONS	21
Total FP COMP	2
Total FN	158

Total Scores
MCC	0.572
Average MCC ± 95% Confidence Intervals	0.522 ± 0.223
Sensitivity	0.399
Positive Predictive Value	0.827
Nr of predictions	8

2. Individual counts for Mastr(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.87	0.80	0.94	16	973	1	0	1	0	4
3RKF_A	Purine links to Rfam database...	0.70	0.50	1.00	17	2194	0	0	0	0	17
3SD1_A	THF links to Rfam database...	0.61	0.50	0.75	21	3888	7	1	6	0	21
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...	0.70	0.59	0.84	32	7102	7	0	6	1	22
4AOB_A	SAM links to Rfam database...	0.39	0.26	0.58	11	4352	9	0	8	1	31
4ENB_A	crcB links to Rfam database...	0.39	0.16	1.00	3	1272	0	0	0	0	16
4ENC_A	crcB links to Rfam database...	0.51	0.26	1.00	5	1321	0	0	0	0	14

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