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 NanoFolder - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

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

Total counts & total scores
Individual counts

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

Overview

Metric	NanoFolder		PPfold(seed)
MCC	0.346	>	0.125
Average MCC ± 95% Confidence Intervals	0.374 ± 0.176	>	0.078 ± 0.162
Sensitivity	0.353	>	0.030
Positive Predictive Value	0.349	<	0.538
Total TP	83	>	7
Total TN	32265	<	32490
Total FP	165	>	25
Total FP CONTRA	21	>	0
Total FP INCONS	134	>	6
Total FP COMP	10	<	19
Total FN	152	<	228
P-value	0.0

Performance plots

Performance of NanoFolder - scored higher 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

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

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

Total Base Pair Counts
Total TP	7
Total TN	32490
Total FP	25
Total FP CONTRA	0
Total FP INCONS	6
Total FP COMP	19
Total FN	228

Total Scores
MCC	0.125
Average MCC ± 95% Confidence Intervals	0.078 ± 0.162
Sensitivity	0.030
Positive Predictive Value	0.538
Nr of predictions	7

2. Individual counts for PPfold(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...	0.47	0.30	0.75	6	1532	2	0	2	0	14
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	2775	0	0	0	0	30
3UZL_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3570	0	0	0	0	37
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.03	0.20	1	11776	23	0	4	19	32
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	42
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.