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 PPfold(seed) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	MXScarna(seed)		PPfold(seed)
MCC	0.624	>	0.102
Average MCC ± 95% Confidence Intervals	0.575 ± 0.167	>	0.050 ± 0.095
Sensitivity	0.493	>	0.020
Positive Predictive Value	0.796	>	0.538
Total TP	176	>	7
Total TN	42687	<	42895
Total FP	61	>	25
Total FP CONTRA	5	>	0
Total FP INCONS	40	>	6
Total FP COMP	16	<	19
Total FN	181	<	350
P-value	1.55268413083e-08

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	176
Total TN	42687
Total FP	61
Total FP CONTRA	5
Total FP INCONS	40
Total FP COMP	16
Total FN	181

Total Scores
MCC	0.624
Average MCC ± 95% Confidence Intervals	0.575 ± 0.167
Sensitivity	0.493
Positive Predictive Value	0.796
Nr of predictions	11

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
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

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.