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 RNAfold - 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 RNAfold & TurboFold(seed) [.zip] - may take several seconds...

Overview

Metric	RNAfold		TurboFold(seed)
MCC	0.578	>	0.550
Average MCC ± 95% Confidence Intervals	0.594 ± 0.189	>	0.555 ± 0.229
Sensitivity	0.502	>	0.456
Positive Predictive Value	0.673	>	0.672
Total TP	142	>	129
Total TN	34339	<	34358
Total FP	81	>	73
Total FP CONTRA	11	>	8
Total FP INCONS	58	>	55
Total FP COMP	12	>	10
Total FN	141	<	154
P-value	0.0

Performance plots

Performance of RNAfold - scored higher in this pairwise comparison

1. Total counts & total scores for RNAfold

Total Base Pair Counts
Total TP	142
Total TN	34339
Total FP	81
Total FP CONTRA	11
Total FP INCONS	58
Total FP COMP	12
Total FN	141

Total Scores
MCC	0.578
Average MCC ± 95% Confidence Intervals	0.594 ± 0.189
Sensitivity	0.502
Positive Predictive Value	0.673
Nr of predictions	9

2. Individual counts for RNAfold [ 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...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
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...	0.64	0.52	0.79	22	3888	6	1	5	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11744	43	5	27	11	28
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
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...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1314	7	1	6	0	14

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	34358
Total FP	73
Total FP CONTRA	8
Total FP INCONS	55
Total FP COMP	10
Total FN	154

Total Scores
MCC	0.550
Average MCC ± 95% Confidence Intervals	0.555 ± 0.229
Sensitivity	0.456
Positive Predictive Value	0.672
Nr of predictions	9

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
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
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.