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

Overview

Metric	Sfold		PPfold(seed)
MCC	0.539	>	0.102
Average MCC ± 95% Confidence Intervals	0.543 ± 0.131	>	0.050 ± 0.095
Sensitivity	0.426	>	0.020
Positive Predictive Value	0.691	>	0.538
Total TP	152	>	7
Total TN	42688	<	42895
Total FP	80	>	25
Total FP CONTRA	8	>	0
Total FP INCONS	60	>	6
Total FP COMP	12	<	19
Total FN	205	<	350
P-value	9.45186852942e-09

Performance plots

Performance of Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP	152
Total TN	42688
Total FP	80
Total FP CONTRA	8
Total FP INCONS	60
Total FP COMP	12
Total FN	205

Total Scores
MCC	0.539
Average MCC ± 95% Confidence Intervals	0.543 ± 0.131
Sensitivity	0.426
Positive Predictive Value	0.691
Nr of predictions	11

2. Individual counts for Sfold [ 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...	0.45	0.35	0.58	7	1528	5	0	5	0	13
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3J16_L	tRNA links to Rfam database...	0.29	0.23	0.37	7	2756	12	0	12	0	23
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...	0.65	0.50	0.84	21	3891	4	1	3	0	21
3UZL_B	tRNA links to Rfam database...	0.51	0.32	0.80	12	3555	3	2	1	0	25
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11751	34	2	23	9	28
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
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...	0.51	0.26	1.00	5	1321	0	0	0	0	14

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	42895
Total FP	25
Total FP CONTRA	0
Total FP INCONS	6
Total FP COMP	19
Total FN	350

Total Scores
MCC	0.102
Average MCC ± 95% Confidence Intervals	0.050 ± 0.095
Sensitivity	0.020
Positive Predictive Value	0.538
Nr of predictions	11

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
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
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.