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 MXScarna(seed) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	CentroidHomfold‑LAST		MXScarna(seed)
MCC	0.634	>	0.621
Average MCC ± 95% Confidence Intervals	0.635 ± 0.173	>	0.575 ± 0.151
Sensitivity	0.501	>	0.496
Positive Predictive Value	0.808	>	0.782
Total TP	189	>	187
Total TN	43664	>	43659
Total FP	54	<	68
Total FP CONTRA	5	=	5
Total FP INCONS	40	<	47
Total FP COMP	9	<	16
Total FN	188	<	190
P-value	9.54564345795e-08

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	189
Total TN	43664
Total FP	54
Total FP CONTRA	5
Total FP INCONS	40
Total FP COMP	9
Total FN	188

Total Scores
MCC	0.634
Average MCC ± 95% Confidence Intervals	0.635 ± 0.173
Sensitivity	0.501
Positive Predictive Value	0.808
Nr of predictions	12

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
3AMU_B	tRNA links to Rfam database...	0.82	0.70	0.95	19	2983	3	0	1	2	8
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
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
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	7104	6	0	6	0	24
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 MXScarna(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	187
Total TN	43659
Total FP	68
Total FP CONTRA	5
Total FP INCONS	47
Total FP COMP	16
Total FN	190

Total Scores
MCC	0.621
Average MCC ± 95% Confidence Intervals	0.575 ± 0.151
Sensitivity	0.496
Positive Predictive Value	0.782
Nr of predictions	12

2. Individual counts for MXScarna(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...	0.57	0.55	0.61	11	972	7	0	7	0	9
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1530	12	0	10	2	20
3AMU_B	tRNA links to Rfam database...	0.84	0.70	1.00	19	2984	1	0	0	1	8
3J16_L	tRNA links to Rfam database...	0.82	0.67	1.00	20	2755	0	0	0	0	10
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...	0.63	0.55	0.74	23	3885	8	1	7	0	19
3UZL_B	tRNA links to Rfam database...	0.66	0.49	0.90	18	3550	2	1	1	0	19
4A1C_3	5S_rRNA links to Rfam database...	0.75	0.65	0.88	35	7100	5	1	4	0	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.35	0.24	0.50	8	11765	20	1	7	12	25
4AOB_A	SAM links to Rfam database...	0.66	0.55	0.79	23	4342	7	0	6	1	19
4ENB_A	crcB links to Rfam database...	0.48	0.32	0.75	6	1267	2	0	2	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	1	3	0	13

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