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 CentroidHomfold‑LAST - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

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

Total counts & total scores
Individual counts

Compile and download dataset for CentroidHomfold‑LAST & RNAalifold(seed) [.zip] - may take several seconds...

Overview

Metric	CentroidHomfold‑LAST		RNAalifold(seed)
MCC	0.573	>	0.529
Average MCC ± 95% Confidence Intervals	0.582 ± 0.272	>	0.502 ± 0.190
Sensitivity	0.450	>	0.349
Positive Predictive Value	0.736	<	0.808
Total TP	103	>	80
Total TN	27270	<	27311
Total FP	44	>	22
Total FP CONTRA	5	>	2
Total FP INCONS	32	>	17
Total FP COMP	7	>	3
Total FN	126	<	149
P-value	0.0

Performance plots

Performance of CentroidHomfold‑LAST - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidHomfold‑LAST

Total Base Pair Counts
Total TP	103
Total TN	27270
Total FP	44
Total FP CONTRA	5
Total FP INCONS	32
Total FP COMP	7
Total FN	126

Total Scores
MCC	0.573
Average MCC ± 95% Confidence Intervals	0.582 ± 0.272
Sensitivity	0.450
Positive Predictive Value	0.736
Nr of predictions	8

2. Individual counts for CentroidHomfold‑LAST [ 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	1529	11	0	11	0	20
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.64	0.45	0.90	19	3895	2	0	2	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.18	5	11753	29	5	18	6	28
4AOB_A	SAM links to Rfam database...	0.71	0.50	1.00	21	4350	1	0	0	1	21
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...	0.76	0.58	1.00	11	1315	0	0	0	0	8

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

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

Total Base Pair Counts
Total TP	80
Total TN	27311
Total FP	22
Total FP CONTRA	2
Total FP INCONS	17
Total FP COMP	3
Total FN	149

Total Scores
MCC	0.529
Average MCC ± 95% Confidence Intervals	0.502 ± 0.190
Sensitivity	0.349
Positive Predictive Value	0.808
Nr of predictions	8

2. Individual counts for RNAalifold(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...	0.59	0.40	0.89	8	981	1	0	1	0	12
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1528	12	0	12	0	20
3RKF_A	Purine links to Rfam database...	0.63	0.47	0.84	16	2192	3	1	2	0	18
3SD1_A	THF links to Rfam database...	0.58	0.40	0.85	17	3896	3	1	2	0	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.39	0.15	1.00	5	11776	2	0	0	2	28
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13

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