CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNASampler(20)		RSpredict(20)
MCC	0.737	>	0.660
Average MCC ± 95% Confidence Intervals	0.750 ± 0.073	>	0.636 ± 0.095
Sensitivity	0.667	>	0.597
Positive Predictive Value	0.820	>	0.735
Total TP	668	>	598
Total TN	104648	<	104649
Total FP	278	<	341
Total FP CONTRA	59	<	84
Total FP INCONS	88	<	132
Total FP COMP	131	>	125
Total FN	333	<	403
P-value	3.56938820447e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	668
Total TN	104648
Total FP	278
Total FP CONTRA	59
Total FP INCONS	88
Total FP COMP	131
Total FN	333

Total Scores
MCC	0.737
Average MCC ± 95% Confidence Intervals	0.750 ± 0.073
Sensitivity	0.667
Positive Predictive Value	0.820
Nr of predictions	39

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2. Individual counts for RNASampler(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...	1.00	1.00	1.00	10	164	0	0	0	0	0
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	14	0	0	14	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	4	1831	2	0	0	2	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...	0.34	0.11	1.00	4	2041	0	0	0	0	31
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...	0.95	0.95	0.95	18	1138	4	0	1	3	1
3GX2_A	SAM links to Rfam database...	0.88	0.79	1.00	22	1427	1	0	0	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...	0.52	0.41	0.65	39	25476	26	15	6	5	56
3IZF_C	5S_rRNA links to Rfam database...	0.92	0.86	1.00	30	2610	2	0	0	2	5
3J20_0	tRNA links to Rfam database...	0.90	0.90	0.90	19	1198	3	1	1	1	2
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.50	0.63	17	2993	12	3	7	2	17
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
3J3E_7	5S_rRNA links to Rfam database...	0.80	0.76	0.84	26	2710	6	0	5	1	8
3J3E_8	5_8S_rRNA links to Rfam database...	0.19	0.20	0.19	3	2726	21	5	8	8	12
3J3F_7	5S_rRNA links to Rfam database...	0.78	0.72	0.84	26	2903	5	0	5	0	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.43	0.47	0.39	9	4738	20	6	8	6	10
3JYV_7	tRNA links to Rfam database...	0.97	0.95	1.00	19	1092	2	0	0	2	1
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	26	10	2	14	2
3JYX_3	5S_rRNA links to Rfam database...	0.70	0.60	0.82	9	2367	14	0	2	12	6
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...	0.75	0.57	1.00	21	2257	5	0	0	5	16
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.50	0.52	11	4743	19	5	5	9	11
3O58_2	5S_rRNA links to Rfam database...	0.93	0.87	1.00	27	2727	5	0	0	5	4
3PDR_A	ykoK links to Rfam database...	0.84	0.76	0.93	38	4799	5	1	2	2	12
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...	0.81	0.69	0.95	20	1512	1	0	1	0	9
3ZEX_D	5S_rRNA links to Rfam database...	0.83	0.69	1.00	24	2772	1	0	0	1	11
3ZEX_C	5_8S_rRNA links to Rfam database...	0.35	0.31	0.39	9	5351	21	3	11	7	20
3ZND_W	tRNA links to Rfam database...	0.58	0.75	0.46	6	1178	18	4	3	11	2
4A1C_3	5S_rRNA links to Rfam database...	0.90	0.81	1.00	30	2733	0	0	0	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	30	3	13	14	15
4AOB_A	SAM links to Rfam database...	0.70	0.59	0.85	17	1417	4	0	3	1	12
4ENB_A	crcB links to Rfam database...	0.68	0.47	1.00	7	465	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	0	0	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.64	0.54	0.76	13	1185	4	0	4	0	11

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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	598
Total TN	104649
Total FP	341
Total FP CONTRA	84
Total FP INCONS	132
Total FP COMP	125
Total FN	403

Total Scores
MCC	0.660
Average MCC ± 95% Confidence Intervals	0.636 ± 0.095
Sensitivity	0.597
Positive Predictive Value	0.735
Nr of predictions	39

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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
3J20_0	tRNA links to Rfam database...	0.90	0.90	0.90	19	1198	3	1	1	1	2
3J20_1	tRNA links to Rfam database...	0.67	0.50	0.91	10	1101	2	0	1	1	10
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.59	0.87	20	2997	6	0	3	3	14
3J3D_C	tRNA links to Rfam database...	0.82	0.84	0.80	16	948	4	3	1	0	3
3J3E_7	5S_rRNA links to Rfam database...	0.82	0.79	0.84	27	2709	7	0	5	2	7
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2724	19	5	13	1	15
3J3F_7	5S_rRNA links to Rfam database...	0.94	0.94	0.94	34	2898	3	1	1	1	2
3J3F_8	5_8S_rRNA links to Rfam database...	0.42	0.47	0.38	9	4737	26	9	6	11	10
3JYV_7	tRNA links to Rfam database...	0.97	0.95	1.00	19	1092	2	0	0	2	1
3JYX_4	5_8S_rRNA links to Rfam database...	0.59	0.75	0.47	9	4737	33	9	1	23	3
3JYX_3	5S_rRNA links to Rfam database...	0.80	0.80	0.80	12	2363	16	0	3	13	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_3	5_8S_rRNA links to Rfam database...	0.38	0.50	0.30	11	4727	29	15	11	3	11
3O58_2	5S_rRNA links to Rfam database...	0.93	0.94	0.94	29	2723	10	0	2	8	2
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
3ZEX_D	5S_rRNA links to Rfam database...	0.88	0.83	0.94	29	2765	7	0	2	5	6
3ZEX_C	5_8S_rRNA links to Rfam database...	0.34	0.31	0.38	9	5350	19	3	12	4	20
3ZND_W	tRNA links to Rfam database...	0.47	0.38	0.60	3	1186	9	0	2	7	5
4A1C_3	5S_rRNA links to Rfam database...	0.60	0.49	0.75	18	2739	8	0	6	2	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.25	0.30	0.21	6	4487	30	12	11	7	14
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.19	0.13	0.33	3	1193	6	1	5	0	21

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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 RNASampler(20) - scored higher in this pairwise comparison

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

2. Individual counts for RNASampler(20) [ 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 ]