CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAalifold(20)		CentroidFold
MCC	0.777	>	0.708
Average MCC ± 95% Confidence Intervals	0.770 ± 0.085	>	0.721 ± 0.101
Sensitivity	0.686	<	0.697
Positive Predictive Value	0.884	>	0.724
Total TP	478	<	486
Total TN	74688	>	74558
Total FP	141	<	278
Total FP CONTRA	21	<	66
Total FP INCONS	42	<	119
Total FP COMP	78	<	93
Total FN	219	>	211
P-value	5.1503931209e-08

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Performance plots

Comparison of performance of RNAalifold(20) and CentroidFold. 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 RNAalifold(20) and CentroidFold).
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 RNAalifold(20) and CentroidFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(20) and CentroidFold. 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 RNAalifold(20) and CentroidFold).

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

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

Total Base Pair Counts
Total TP	478
Total TN	74688
Total FP	141
Total FP CONTRA	21
Total FP INCONS	42
Total FP COMP	78
Total FN	219

Total Scores
MCC	0.777
Average MCC ± 95% Confidence Intervals	0.770 ± 0.085
Sensitivity	0.686
Positive Predictive Value	0.884
Nr of predictions	26

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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...	0.51	0.50	0.56	9	341	8	0	7	1	9
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	12	0	0	12	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	4	1831	3	0	0	3	7
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.44	0.20	1.00	7	2038	0	0	0	0	28
3A2K_C	tRNA links to Rfam database...	0.98	0.95	1.00	21	1087	0	0	0	0	1
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	2	0	0	2	0
3GX2_A	SAM links to Rfam database...	0.92	0.86	1.00	24	1425	1	0	0	1	4
3IVN_B	Purine links to Rfam database...	0.86	0.78	0.95	18	884	1	1	0	0	5
3IZ4_A	tmRNA links to Rfam database...	0.65	0.48	0.87	46	25483	15	4	3	8	49
3IZF_C	5S_rRNA links to Rfam database...	0.90	0.89	0.91	31	2606	6	0	3	3	4
3JYV_7	tRNA links to Rfam database...	0.97	0.95	1.00	19	1092	2	0	0	2	1
3JYX_3	5S_rRNA links to Rfam database...	0.76	0.73	0.79	11	2364	20	0	3	17	4
3JYX_4	5_8S_rRNA links to Rfam database...	0.77	0.83	0.71	10	4742	15	3	1	11	2
3LA5_A	Purine links to Rfam database...	0.87	0.76	1.00	19	935	0	0	0	0	6
3NPB_A	SAM links to Rfam database...	0.75	0.57	1.00	21	2257	4	0	0	4	16
3O58_2	5S_rRNA links to Rfam database...	0.97	0.94	1.00	29	2725	7	0	0	7	2
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.36	0.50	8	4748	9	3	5	1	14
3PDR_A	ykoK links to Rfam database...	0.92	0.88	0.96	44	4794	3	1	1	1	6
3RKF_A	Purine links to Rfam database...	0.81	0.71	0.94	17	848	1	0	1	0	7
3SD1_A	THF links to Rfam database...	0.84	0.86	0.83	25	1503	5	4	1	0	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.19	5	4490	23	5	16	2	15
4A1C_3	5S_rRNA links to Rfam database...	0.90	0.84	0.97	31	2731	1	0	1	0	6
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	2	0	0	2	8
4ENB_A	crcB links to Rfam database...	0.51	0.27	1.00	4	468	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.63	0.40	1.00	6	490	0	0	0	0	9

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Performance of CentroidFold - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidFold

Total Base Pair Counts
Total TP	486
Total TN	74558
Total FP	278
Total FP CONTRA	66
Total FP INCONS	119
Total FP COMP	93
Total FN	211

Total Scores
MCC	0.708
Average MCC ± 95% Confidence Intervals	0.721 ± 0.101
Sensitivity	0.697
Positive Predictive Value	0.724
Nr of predictions	26

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2. Individual counts for CentroidFold [ 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...	0.94	0.94	0.94	17	339	2	0	1	1	1
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	13	0	0	13	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	27	0	6	21	3
2XQD_Y	tRNA links to Rfam database...	0.83	0.81	0.85	17	1109	4	0	3	1	4
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.13	0.11	0.17	4	2021	21	2	18	1	31
3A2K_C	tRNA links to Rfam database...	0.49	0.55	0.46	12	1082	14	3	11	0	10
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3GX2_A	SAM links to Rfam database...	0.94	0.89	1.00	25	1424	1	0	0	1	3
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IZ4_A	tmRNA links to Rfam database...	0.60	0.57	0.64	54	25451	38	16	15	7	41
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	11	0	5	6	3
3JYV_7	tRNA links to Rfam database...	0.92	0.85	1.00	17	1094	2	0	0	2	3
3JYX_3	5S_rRNA links to Rfam database...	0.35	0.47	0.27	7	2352	21	14	5	2	8
3JYX_4	5_8S_rRNA links to Rfam database...	0.41	0.58	0.29	7	4732	25	11	6	8	5
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NPB_A	SAM links to Rfam database...	0.87	0.84	0.91	31	2244	8	1	2	5	6
3O58_2	5S_rRNA links to Rfam database...	0.95	0.94	0.97	29	2724	7	0	1	6	2
3O58_3	5_8S_rRNA links to Rfam database...	0.44	0.41	0.47	9	4745	11	1	9	1	13
3PDR_A	ykoK links to Rfam database...	0.88	0.86	0.90	43	4792	7	2	3	2	7
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.70	0.69	0.71	20	1505	8	4	4	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.19	5	4490	29	9	12	8	15
4A1C_3	5S_rRNA links to Rfam database...	0.80	0.78	0.83	29	2728	8	0	6	2	8
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	1	0	0	1	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	1	0	0	1	4

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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 RNAalifold(20) - scored higher in this pairwise comparison

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

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

Performance of CentroidFold - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidFold

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