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 RNAalifold(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of Cylofold - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	RNAalifold(20)		Cylofold
MCC	0.668	>	0.608
Average MCC ± 95% Confidence Intervals	0.635 ± 0.099	<	0.640 ± 0.145
Sensitivity	0.509	<	0.523
Positive Predictive Value	0.880	>	0.712
Total TP	250	<	257
Total TN	68815	>	68738
Total FP	41	<	128
Total FP CONTRA	7	<	19
Total FP INCONS	27	<	85
Total FP COMP	7	<	24
Total FN	241	>	234
P-value	2.66715895098e-08

Performance plots

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

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

Total Base Pair Counts
Total TP	250
Total TN	68815
Total FP	41
Total FP CONTRA	7
Total FP INCONS	27
Total FP COMP	7
Total FN	241

Total Scores
MCC	0.668
Average MCC ± 95% Confidence Intervals	0.635 ± 0.099
Sensitivity	0.509
Positive Predictive Value	0.880
Nr of predictions	14

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.53	0.50	0.59	10	973	7	0	7	0	10
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	4	4556	3	0	0	3	16
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.41	0.17	1.00	7	5144	0	0	0	0	35
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	1	0	0	1	7
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.59	0.86	32	6866	5	1	4	0	22
3O58_2	5S_rRNA links to Rfam database...	0.79	0.76	0.83	29	7225	7	3	3	1	9
3O58_3	5_8S_rRNA links to Rfam database...	0.37	0.26	0.53	9	12386	8	2	6	0	26
3PDR_A	ykoK links to Rfam database...	0.76	0.61	0.96	44	12834	3	0	2	1	28
3RKF_A	Purine links to Rfam database...	0.68	0.50	0.94	17	2193	1	0	1	0	17
3SD1_A	THF links to Rfam database...	0.70	0.60	0.83	25	3886	5	1	4	0	17
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENB_A	crcB links to Rfam database...	0.46	0.21	1.00	4	1271	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13

Performance of Cylofold - scored lower in this pairwise comparison

1. Total counts & total scores for Cylofold

Total Base Pair Counts
Total TP	257
Total TN	68738
Total FP	128
Total FP CONTRA	19
Total FP INCONS	85
Total FP COMP	24
Total FN	234

Total Scores
MCC	0.608
Average MCC ± 95% Confidence Intervals	0.640 ± 0.145
Sensitivity	0.523
Positive Predictive Value	0.712
Nr of predictions	14

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
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.38	0.40	0.36	8	4538	23	7	7	9	12
2XQD_Y	tRNA links to Rfam database...	0.81	0.78	0.84	21	2825	4	4	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.10	0.10	0.11	4	5115	32	1	31	0	38
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	6867	6	0	6	0	24
3O58_2	5S_rRNA links to Rfam database...	0.80	0.68	0.93	26	7232	3	0	2	1	12
3O58_3	5_8S_rRNA links to Rfam database...	0.36	0.34	0.38	12	12371	29	5	15	9	23
3PDR_A	ykoK links to Rfam database...	0.72	0.54	0.95	39	12839	4	0	2	2	33
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
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

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