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 Carnac(20) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for CentroidHomfold‑LAST & Carnac(20) [.zip] - may take several seconds...

Overview

Metric	CentroidHomfold‑LAST		Carnac(20)
MCC	0.654	>	0.540
Average MCC ± 95% Confidence Intervals	0.685 ± 0.163	>	0.393 ± 0.246
Sensitivity	0.524	>	0.341
Positive Predictive Value	0.822	<	0.861
Total TP	152	>	99
Total TN	35828	<	35898
Total FP	42	>	20
Total FP CONTRA	5	>	1
Total FP INCONS	28	>	15
Total FP COMP	9	>	4
Total FN	138	<	191
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	152
Total TN	35828
Total FP	42
Total FP CONTRA	5
Total FP INCONS	28
Total FP COMP	9
Total FN	138

Total Scores
MCC	0.654
Average MCC ± 95% Confidence Intervals	0.685 ± 0.163
Sensitivity	0.524
Positive Predictive Value	0.822
Nr of predictions	9

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
3AMU_B	tRNA links to Rfam database...	0.82	0.70	0.95	19	2983	3	0	1	2	8
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
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	7104	6	0	6	0	24
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 Carnac(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	99
Total TN	35898
Total FP	20
Total FP CONTRA	1
Total FP INCONS	15
Total FP COMP	4
Total FN	191

Total Scores
MCC	0.540
Average MCC ± 95% Confidence Intervals	0.393 ± 0.246
Sensitivity	0.341
Positive Predictive Value	0.861
Nr of predictions	9

2. Individual counts for Carnac(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...	0.00	0.00	0.00	0	990	0	0	0	0	20
3AMU_B	tRNA links to Rfam database...	0.69	0.59	0.80	16	2983	6	0	4	2	11
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...	0.60	0.38	0.94	16	3899	1	0	1	0	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.15	0.71	5	11774	3	0	2	1	28
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...	0.49	0.33	0.74	14	4352	6	1	4	1	28
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.