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(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

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

Total counts & total scores
Individual counts

Compile and download dataset for MXScarna(20) & Murlet(seed) [.zip] - may take several seconds...

Overview

Metric	MXScarna(20)		Murlet(seed)
MCC	0.625	>	0.491
Average MCC ± 95% Confidence Intervals	0.614 ± 0.106	>	0.494 ± 0.047
Sensitivity	0.506	>	0.269
Positive Predictive Value	0.775	<	0.901
Total TP	290	>	154
Total TN	89365	<	89568
Total FP	139	>	23
Total FP CONTRA	10	>	5
Total FP INCONS	74	>	12
Total FP COMP	55	>	6
Total FN	283	<	419
P-value	3.18846395401e-08

Performance plots

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

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

Total Base Pair Counts
Total TP	290
Total TN	89365
Total FP	139
Total FP CONTRA	10
Total FP INCONS	74
Total FP COMP	55
Total FN	283

Total Scores
MCC	0.625
Average MCC ± 95% Confidence Intervals	0.614 ± 0.106
Sensitivity	0.506
Positive Predictive Value	0.775
Nr of predictions	17

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.73	0.70	0.78	14	972	4	0	4	0	6
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	4	4556	3	0	0	3	16
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.80	0.71	0.91	30	5118	4	0	3	1	12
3GX2_A	SAM links to Rfam database...	0.70	0.58	0.85	23	4344	5	0	4	1	17
3IVN_B	Purine links to Rfam database...	0.74	0.58	0.95	18	2327	1	1	0	0	13
3JYX_4	5_8S_rRNA links to Rfam database...	0.33	0.30	0.37	10	12219	32	2	15	15	23
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.69	0.59	0.82	27	6988	9	1	5	3	19
3O58_3	5_8S_rRNA links to Rfam database...	0.52	0.40	0.67	14	12382	17	2	5	10	21
3PDR_A	ykoK links to Rfam database...	0.71	0.57	0.89	41	12834	9	0	5	4	31
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	2	6	0	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	36	2	17	17	28
4AOB_A	SAM links to Rfam database...	0.62	0.55	0.72	23	4339	10	0	9	1	19
4ENB_A	crcB links to Rfam database...	0.26	0.11	0.67	2	1272	1	0	1	0	17
4ENC_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1319	0	0	0	0	12

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

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

Total Base Pair Counts
Total TP	154
Total TN	89568
Total FP	23
Total FP CONTRA	5
Total FP INCONS	12
Total FP COMP	6
Total FN	419

Total Scores
MCC	0.491
Average MCC ± 95% Confidence Intervals	0.494 ± 0.047
Sensitivity	0.269
Positive Predictive Value	0.901
Nr of predictions	17

2. Individual counts for Murlet(seed) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.52	0.27	1.00	3	403	0	0	0	0	8
2L94_A	HIV_FE links to Rfam database...	0.59	0.40	0.89	8	981	1	0	1	0	12
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	4	4556	2	0	0	2	16
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.38	0.14	1.00	6	5145	0	0	0	0	36
3GX2_A	SAM links to Rfam database...	0.59	0.35	1.00	14	4357	1	0	0	1	26
3IVN_B	Purine links to Rfam database...	0.53	0.39	0.75	12	2330	4	2	2	0	19
3JYX_4	5_8S_rRNA links to Rfam database...	0.23	0.09	0.60	3	12241	4	0	2	2	30
3LA5_A	Purine links to Rfam database...	0.58	0.41	0.82	14	2468	3	1	2	0	20
3NPB_A	SAM links to Rfam database...	0.49	0.28	0.87	13	7006	2	1	1	0	33
3O58_3	5_8S_rRNA links to Rfam database...	0.45	0.20	1.00	7	12396	0	0	0	0	28
3PDR_A	ykoK links to Rfam database...	0.44	0.19	1.00	14	12866	0	0	0	0	58
3RKF_A	Purine links to Rfam database...	0.53	0.35	0.80	12	2196	3	1	2	0	22
3SD1_A	THF links to Rfam database...	0.47	0.26	0.85	11	3903	2	0	2	0	31
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	11774	0	0	0	0	26
4AOB_A	SAM links to Rfam database...	0.58	0.33	1.00	14	4357	1	0	0	1	28
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13

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