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 RNASampler(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

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

Total counts & total scores
Individual counts

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

Overview

Metric	RNASampler(20)		TurboFold(seed)
MCC	0.642	>	0.595
Average MCC ± 95% Confidence Intervals	0.654 ± 0.182	>	0.626 ± 0.187
Sensitivity	0.487	<	0.490
Positive Predictive Value	0.853	>	0.729
Total TP	128	<	129
Total TN	32860	>	32833
Total FP	36	<	58
Total FP CONTRA	0	<	6
Total FP INCONS	22	<	42
Total FP COMP	14	>	10
Total FN	135	>	134
P-value	0.0

Performance plots

Performance of RNASampler(20) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	128
Total TN	32860
Total FP	36
Total FP CONTRA	0
Total FP INCONS	22
Total FP COMP	14
Total FN	135

Total Scores
MCC	0.642
Average MCC ± 95% Confidence Intervals	0.654 ± 0.182
Sensitivity	0.487
Positive Predictive Value	0.853
Nr of predictions	8

2. Individual counts for RNASampler(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...	0.92	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...	0.67	0.48	0.95	20	3895	1	0	1	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.23	5	11759	30	0	17	13	28
4A1C_3	5S_rRNA links to Rfam database...	0.74	0.56	1.00	30	7110	0	0	0	0	24
4AOB_A	SAM links to Rfam database...	0.58	0.40	0.85	17	4351	4	0	3	1	25
4ENB_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1268	0	0	0	0	12
4ENC_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1315	0	0	0	0	8

Performance of TurboFold(seed) - scored lower 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

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