CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	HotKnots		RSpredict(20)
MCC	0.694	>	0.663
Average MCC ± 95% Confidence Intervals	0.733 ± 0.109	>	0.653 ± 0.116
Sensitivity	0.716	>	0.593
Positive Predictive Value	0.678	<	0.748
Total TP	506	>	419
Total TN	74657	<	74843
Total FP	363	>	230
Total FP CONTRA	86	>	61
Total FP INCONS	154	>	80
Total FP COMP	123	>	89
Total FN	201	<	288
P-value	5.1503931209e-08

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Performance plots

Comparison of performance of HotKnots 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 HotKnots 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 HotKnots and RSpredict(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for HotKnots 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 HotKnots and RSpredict(20)).

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Performance of HotKnots - scored higher in this pairwise comparison

1. Total counts & total scores for HotKnots

Total Base Pair Counts
Total TP	506
Total TN	74657
Total FP	363
Total FP CONTRA	86
Total FP INCONS	154
Total FP COMP	123
Total FN	201

Total Scores
MCC	0.694
Average MCC ± 95% Confidence Intervals	0.733 ± 0.109
Sensitivity	0.716
Positive Predictive Value	0.678
Nr of predictions	27

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2. Individual counts for HotKnots [ 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...	1.00	1.00	1.00	10	164	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	25	0	6	19	3
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...	0.35	0.34	0.38	12	2013	21	1	19	1	23
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
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...	0.81	0.79	0.85	22	1423	5	2	2	1	6
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...	0.56	0.60	0.52	57	25426	57	26	27	4	38
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	9	0	5	4	3
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1089	22	4	18	0	20
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	27	0	4	23	3
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	31	10	2	19	2
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...	0.85	0.78	0.94	29	2247	6	0	2	4	8
3O58_2	5S_rRNA links to Rfam database...	0.87	0.87	0.87	27	2723	12	0	4	8	4
3O58_3	5_8S_rRNA links to Rfam database...	0.26	0.36	0.19	8	4722	35	16	18	1	14
3PDR_A	ykoK links to Rfam database...	0.81	0.80	0.82	40	4791	11	3	6	2	10
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...	0.77	0.76	0.79	22	1505	6	4	2	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	42	12	16	14	15
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	7	0	4	3	5
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

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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	419
Total TN	74843
Total FP	230
Total FP CONTRA	61
Total FP INCONS	80
Total FP COMP	89
Total FN	288

Total Scores
MCC	0.663
Average MCC ± 95% Confidence Intervals	0.653 ± 0.116
Sensitivity	0.593
Positive Predictive Value	0.748
Nr of predictions	27

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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...	0.89	0.80	1.00	8	166	0	0	0	0	2
2L94_A	HIV_FE links to Rfam database...	0.53	0.50	0.60	9	342	7	0	6	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...	0.00	0.00	0.00	0	1831	4	1	3	0	11
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...	0.50	0.26	1.00	9	2036	0	0	0	0	26
3A2K_C	tRNA links to Rfam database...	0.88	0.86	0.90	19	1087	2	0	2	0	3
3AMU_B	tRNA links to Rfam database...	0.69	0.53	0.91	10	1146	2	0	1	1	9
3GX2_A	SAM links to Rfam database...	0.40	0.21	0.75	6	1441	2	1	1	0	22
3IVN_B	Purine links to Rfam database...	0.91	0.87	0.95	20	882	1	1	0	0	3
3IZ4_A	tmRNA links to Rfam database...	0.61	0.57	0.67	54	25455	38	13	14	11	41
3IZF_C	5S_rRNA links to Rfam database...	0.94	0.91	0.97	32	2607	4	0	1	3	3
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...	0.80	0.80	0.80	12	2363	16	0	3	13	3
3JYX_4	5_8S_rRNA links to Rfam database...	0.59	0.75	0.47	9	4737	33	9	1	23	3
3LA5_A	Purine links to Rfam database...	0.89	0.80	1.00	20	934	0	0	0	0	5
3NPB_A	SAM links to Rfam database...	-0.01	0.00	0.00	0	2272	6	1	5	0	37
3O58_2	5S_rRNA links to Rfam database...	0.93	0.94	0.94	29	2723	10	0	2	8	2
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.50	0.30	11	4727	29	15	11	3	11
3PDR_A	ykoK links to Rfam database...	0.80	0.70	0.92	35	4802	5	1	2	2	15
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	1	0	0	3
3SD1_A	THF links to Rfam database...	0.82	0.86	0.78	25	1501	7	5	2	0	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.25	0.30	0.21	6	4487	30	12	11	7	14
4A1C_3	5S_rRNA links to Rfam database...	0.60	0.49	0.75	18	2739	8	0	6	2	19
4AOB_A	SAM links to Rfam database...	0.33	0.21	0.55	6	1426	5	1	4	0	23
4ENB_A	crcB links to Rfam database...	0.54	0.40	0.75	6	464	2	0	2	0	9
4ENC_A	crcB links to Rfam database...	0.51	0.40	0.67	6	487	3	0	3	0	9

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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 HotKnots - scored higher in this pairwise comparison

1. Total counts & total scores for HotKnots

2. Individual counts for HotKnots [ 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 ]