CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAsubopt		RSpredict(20)
MCC	0.560	>	0.559
Average MCC ± 95% Confidence Intervals	0.571 ± 0.100	>	0.566 ± 0.099
Sensitivity	0.502	>	0.446
Positive Predictive Value	0.629	<	0.705
Total TP	465	>	413
Total TN	191285	<	191438
Total FP	322	>	207
Total FP CONTRA	47	>	42
Total FP INCONS	227	>	131
Total FP COMP	48	>	34
Total FN	462	<	514
P-value	0.590817397584

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Performance plots

Comparison of performance of RNAsubopt and RSpredict(20). Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for RNAsubopt and RSpredict(20)).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for RNAsubopt and RSpredict(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAsubopt and RSpredict(20). The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for RNAsubopt and RSpredict(20)).

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Performance of RNAsubopt - scored higher in this pairwise comparison

1. Total counts & total scores for RNAsubopt

Total Base Pair Counts
Total TP	465
Total TN	191285
Total FP	322
Total FP CONTRA	47
Total FP INCONS	227
Total FP COMP	48
Total FN	462

Total Scores
MCC	0.560
Average MCC ± 95% Confidence Intervals	0.571 ± 0.100
Sensitivity	0.502
Positive Predictive Value	0.629
Nr of predictions	24

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2. Individual counts for RNAsubopt [ 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
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	12	5	3	4	7
2XQD_Y	tRNA links to Rfam database...	0.75	0.67	0.86	18	2829	3	0	3	0	9
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3GX2_A	SAM links to Rfam database...	0.44	0.38	0.54	15	4343	14	1	12	1	25
3IVN_B	Purine links to Rfam database...	0.76	0.58	1.00	18	2328	0	0	0	0	13
3IZ4_A	tmRNA links to Rfam database...	0.51	0.47	0.56	62	70766	49	8	40	1	70
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.61	0.80	33	6862	8	1	7	0	21
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2829	21	0	21	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.19	0.21	0.17	7	12204	38	11	24	3	26
3JYX_3	5S_rRNA links to Rfam database...	0.63	0.63	0.63	17	6301	21	1	9	11	10
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...	0.75	0.65	0.86	30	6986	7	1	4	2	16
3O58_2	5S_rRNA links to Rfam database...	0.72	0.74	0.70	28	7220	13	4	8	1	10
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	34	2	21	11	23
3PDR_A	ykoK links to Rfam database...	0.75	0.63	0.90	45	12830	7	1	4	2	27
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	0.50	0.75	21	3888	7	1	6	0	21
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.13	5	11742	43	5	29	9	28
4AOB_A	SAM links to Rfam database...	0.52	0.43	0.64	18	4343	11	2	8	1	24
4ENB_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1314	7	0	7	0	14

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Performance of RSpredict(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	413
Total TN	191438
Total FP	207
Total FP CONTRA	42
Total FP INCONS	131
Total FP COMP	34
Total FN	514

Total Scores
MCC	0.559
Average MCC ± 95% Confidence Intervals	0.566 ± 0.099
Sensitivity	0.446
Positive Predictive Value	0.705
Nr of predictions	24

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2. Individual counts for RSpredict(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...	0.85	0.73	1.00	8	398	0	0	0	0	3
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	11	5	3	3	7
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
3A2K_C	tRNA links to Rfam database...	0.78	0.68	0.90	19	2905	2	0	2	0	9
3AMU_B	tRNA links to Rfam database...	0.61	0.41	0.92	11	2991	1	0	1	0	16
3GX2_A	SAM links to Rfam database...	0.33	0.15	0.75	6	4363	2	0	2	0	34
3IVN_B	Purine links to Rfam database...	0.78	0.65	0.95	20	2325	1	0	1	0	11
3IZ4_A	tmRNA links to Rfam database...	0.53	0.43	0.65	57	70788	35	8	23	4	75
3IZF_C	5S_rRNA links to Rfam database...	0.75	0.61	0.92	33	6867	3	1	2	0	21
3JYV_7	tRNA links to Rfam database...	0.77	0.63	0.95	20	2829	1	0	1	0	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.28	0.27	0.30	9	12216	33	5	16	12	24
3JYX_3	5S_rRNA links to Rfam database...	0.61	0.56	0.68	15	6306	13	0	7	6	12
3LA5_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2465	0	0	0	0	14
3NPB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	7015	6	1	5	0	46
3O58_2	5S_rRNA links to Rfam database...	0.76	0.76	0.76	29	7222	10	3	6	1	9
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.34	0.30	12	12363	28	12	16	0	23
3PDR_A	ykoK links to Rfam database...	0.67	0.49	0.92	35	12842	5	0	3	2	37
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.68	0.60	0.78	25	3884	7	1	6	0	17
4A1C_3	5S_rRNA links to Rfam database...	0.48	0.33	0.69	18	7114	8	0	8	0	36
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.18	0.20	6	11751	30	6	18	6	27
4AOB_A	SAM links to Rfam database...	0.28	0.14	0.55	6	4360	5	0	5	0	36
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...	0.45	0.32	0.67	6	1317	3	0	3	0	13

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

Table of contents:

Overview

Performance plots

Performance of RNAsubopt - scored higher in this pairwise comparison

1. Total counts & total scores for RNAsubopt

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

Performance of RSpredict(20) - scored lower in this pairwise comparison

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

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