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 PPfold(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of IPknot - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for PPfold(20) & IPknot [.zip] - may take several seconds...

Overview

Metric	PPfold(20)		IPknot
MCC	0.665	>	0.571
Average MCC ± 95% Confidence Intervals	0.640 ± 0.167	>	0.581 ± 0.171
Sensitivity	0.519	>	0.463
Positive Predictive Value	0.859	>	0.710
Total TP	140	>	125
Total TN	34860	>	34847
Total FP	29	<	59
Total FP CONTRA	0	<	6
Total FP INCONS	23	<	45
Total FP COMP	6	<	8
Total FN	130	<	145
P-value	0.0

Performance plots

Performance of PPfold(20) - scored higher in this pairwise comparison

1. Total counts & total scores for PPfold(20)

Total Base Pair Counts
Total TP	140
Total TN	34860
Total FP	29
Total FP CONTRA	0
Total FP INCONS	23
Total FP COMP	6
Total FN	130

Total Scores
MCC	0.665
Average MCC ± 95% Confidence Intervals	0.640 ± 0.167
Sensitivity	0.519
Positive Predictive Value	0.859
Nr of predictions	8

2. Individual counts for PPfold(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	1	0	0	1	7
3RKF_A	Purine links to Rfam database...	0.73	0.56	0.95	19	2191	1	0	1	0	15
3SD1_A	THF links to Rfam database...	0.68	0.52	0.88	22	3891	3	0	3	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.15	0.29	5	11764	16	0	12	4	28
4A1C_3	5S_rRNA links to Rfam database...	0.77	0.63	0.94	34	7104	2	0	2	0	20
4AOB_A	SAM links to Rfam database...	0.74	0.60	0.93	25	4344	3	0	2	1	17
4ENB_A	crcB links to Rfam database...	0.56	0.37	0.88	7	1267	1	0	1	0	12
4ENC_A	crcB links to Rfam database...	0.58	0.42	0.80	8	1316	2	0	2	0	11

Performance of IPknot - scored lower in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	125
Total TN	34847
Total FP	59
Total FP CONTRA	6
Total FP INCONS	45
Total FP COMP	8
Total FN	145

Total Scores
MCC	0.571
Average MCC ± 95% Confidence Intervals	0.581 ± 0.171
Sensitivity	0.463
Positive Predictive Value	0.710
Nr of predictions	8

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
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...	0.61	0.48	0.80	20	3891	5	0	5	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	26	4	17	5	28
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
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...	0.52	0.42	0.67	8	1314	4	0	4	0	11

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