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 MXScarna(seed) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of NanoFolder - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	MXScarna(seed)		NanoFolder
MCC	0.594	>	0.346
Average MCC ± 95% Confidence Intervals	0.521 ± 0.266	>	0.374 ± 0.176
Sensitivity	0.468	>	0.353
Positive Predictive Value	0.759	>	0.349
Total TP	110	>	83
Total TN	32358	>	32265
Total FP	50	<	165
Total FP CONTRA	4	<	21
Total FP INCONS	31	<	134
Total FP COMP	15	>	10
Total FN	125	<	152
P-value	0.0

Performance plots

Performance of MXScarna(seed) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	110
Total TN	32358
Total FP	50
Total FP CONTRA	4
Total FP INCONS	31
Total FP COMP	15
Total FN	125

Total Scores
MCC	0.594
Average MCC ± 95% Confidence Intervals	0.521 ± 0.266
Sensitivity	0.468
Positive Predictive Value	0.759
Nr of predictions	7

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
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1530	12	0	10	2	20
3J16_L	tRNA links to Rfam database...	0.82	0.67	1.00	20	2755	0	0	0	0	10
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
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	1	3	0	13

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	83
Total TN	32265
Total FP	165
Total FP CONTRA	21
Total FP INCONS	134
Total FP COMP	10
Total FN	152

Total Scores
MCC	0.346
Average MCC ± 95% Confidence Intervals	0.374 ± 0.176
Sensitivity	0.353
Positive Predictive Value	0.349
Nr of predictions	7

2. Individual counts for NanoFolder [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.52	0.55	0.50	11	1518	11	0	11	0	9
3J16_L	tRNA links to Rfam database...	0.36	0.37	0.37	11	2745	19	3	16	0	19
3UZL_B	tRNA links to Rfam database...	0.36	0.35	0.38	13	3536	21	3	18	0	24
4A1C_3	5S_rRNA links to Rfam database...	0.48	0.46	0.51	25	7091	24	2	22	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11728	61	12	41	8	33
4AOB_A	SAM links to Rfam database...	0.33	0.29	0.39	12	4340	20	1	18	1	30
4ENC_A	crcB links to Rfam database...	0.57	0.58	0.58	11	1307	9	0	8	1	8

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