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 Cylofold - 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 Cylofold & PPfold(seed) [.zip] - may take several seconds...

Overview

Metric	Cylofold		PPfold(seed)
MCC	0.630	>	0.128
Average MCC ± 95% Confidence Intervals	0.662 ± 0.138	>	0.052 ± 0.121
Sensitivity	0.519	>	0.022
Positive Predictive Value	0.773	>	0.750
Total TP	140	>	6
Total TN	23806	<	23979
Total FP	44	>	2
Total FP CONTRA	3	>	0
Total FP INCONS	38	>	2
Total FP COMP	3	>	0
Total FN	130	<	264
P-value	0.0

Performance plots

Performance of Cylofold - scored higher in this pairwise comparison

1. Total counts & total scores for Cylofold

Total Base Pair Counts
Total TP	140
Total TN	23806
Total FP	44
Total FP CONTRA	3
Total FP INCONS	38
Total FP COMP	3
Total FN	130

Total Scores
MCC	0.630
Average MCC ± 95% Confidence Intervals	0.662 ± 0.138
Sensitivity	0.519
Positive Predictive Value	0.773
Nr of predictions	9

2. Individual counts for Cylofold [ 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...	0.61	0.55	0.69	11	1524	5	0	5	0	9
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
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...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.62	0.50	0.78	21	3889	6	0	6	0	21
3UZL_B	tRNA links to Rfam database...	0.45	0.38	0.54	14	3544	12	1	11	0	23
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

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

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

Total Base Pair Counts
Total TP	6
Total TN	23979
Total FP	2
Total FP CONTRA	0
Total FP INCONS	2
Total FP COMP	0
Total FN	264

Total Scores
MCC	0.128
Average MCC ± 95% Confidence Intervals	0.052 ± 0.121
Sensitivity	0.022
Positive Predictive Value	0.750
Nr of predictions	9

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
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3003	0	0	0	0	27
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	2775	0	0	0	0	30
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2211	0	0	0	0	34
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	42
3UZL_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3570	0	0	0	0	37
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	42
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.