CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

Overview

Metric	Carnac(20)		Contrafold
MCC	0.590	>	0.536
Average MCC ± 95% Confidence Intervals	0.566 ± 0.072	>	0.546 ± 0.080
Sensitivity	0.389	<	0.472
Positive Predictive Value	0.899	>	0.613
Total TP	585	<	710
Total TN	284056	>	283548
Total FP	92	<	526
Total FP CONTRA	9	<	58
Total FP INCONS	57	<	391
Total FP COMP	26	<	77
Total FN	919	>	794
P-value	3.56938820447e-08

^top

Performance plots

Comparison of performance of Carnac(20) and Contrafold. 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 Carnac(20) and Contrafold).
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 Carnac(20) and Contrafold).
Comparison of average Matthews Correlation Coefficients (MCCs) for Carnac(20) and Contrafold. 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 Carnac(20) and Contrafold).

^top

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

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

Total Base Pair Counts
Total TP	585
Total TN	284056
Total FP	92
Total FP CONTRA	9
Total FP INCONS	57
Total FP COMP	26
Total FN	919

Total Scores
MCC	0.590
Average MCC ± 95% Confidence Intervals	0.566 ± 0.072
Sensitivity	0.389
Positive Predictive Value	0.899
Nr of predictions	38

^top

2. Individual counts for Carnac(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...	0.73	0.55	1.00	6	400	0	0	0	0	5
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2XQD_Y	tRNA links to Rfam database...	0.79	0.63	1.00	17	2833	0	0	0	0	10
3A2K_C	tRNA links to Rfam database...	0.78	0.61	1.00	17	2909	0	0	0	0	11
3AMU_B	tRNA links to Rfam database...	0.69	0.59	0.80	16	2983	6	0	4	2	11
3G4S_9	5S_rRNA links to Rfam database...	0.50	0.28	0.89	16	7363	2	1	1	0	41
3GX2_A	SAM links to Rfam database...	0.57	0.33	1.00	13	4358	0	0	0	0	27
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IZ4_A	tmRNA links to Rfam database...	0.47	0.23	0.94	31	70843	2	0	2	0	101
3IZF_C	5S_rRNA links to Rfam database...	0.73	0.56	0.97	30	6872	1	0	1	0	24
3J20_0	tRNA links to Rfam database...	0.62	0.53	0.73	16	2828	7	0	6	1	14
3J20_1	tRNA links to Rfam database...	0.86	0.74	1.00	17	2909	0	0	0	0	6
3J2L_3	5S_rRNA links to Rfam database...	0.46	0.34	0.64	18	7847	11	0	10	1	35
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3J3E_7	5S_rRNA links to Rfam database...	0.65	0.44	0.96	24	7115	1	0	1	0	30
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7503	0	0	0	0	33
3J3F_7	5S_rRNA links to Rfam database...	0.66	0.44	1.00	22	7238	0	0	0	0	28
3J3F_8	5_8S_rRNA links to Rfam database...	0.50	0.25	1.00	9	12237	0	0	0	0	27
3J3V_B	5S_rRNA links to Rfam database...	0.58	0.35	0.95	20	7000	1	0	1	0	37
3JYV_7	tRNA links to Rfam database...	0.68	0.50	0.94	16	2833	1	0	1	0	16
3JYX_4	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	12239	2	0	0	2	26
3JYX_3	5S_rRNA links to Rfam database...	0.64	0.56	0.75	15	6308	10	1	4	5	12
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...	0.44	0.20	1.00	9	7012	2	0	0	2	37
3O58_2	5S_rRNA links to Rfam database...	0.83	0.71	0.96	27	7232	2	0	1	1	11
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.26	1.00	9	12394	0	0	0	0	26
3PDR_A	ykoK links to Rfam database...	0.62	0.40	0.97	29	12850	3	0	1	2	43
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...	0.60	0.38	0.94	16	3899	1	0	1	0	26
3ZEX_D	5S_rRNA links to Rfam database...	0.73	0.53	1.00	26	6995	0	0	0	0	23
3ZEX_C	5_8S_rRNA links to Rfam database...	0.31	0.13	0.70	7	14186	3	1	2	0	45
3ZND_W	tRNA links to Rfam database...	0.47	0.39	0.56	9	2987	10	0	7	3	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.15	0.71	5	11774	3	0	2	1	28
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4AOB_A	SAM links to Rfam database...	0.49	0.33	0.74	14	4352	6	1	4	1	28
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19
4FRG_B	AdoCbl-variant links to Rfam database...	0.43	0.19	1.00	6	3480	0	0	0	0	26

^top

Performance of Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP	710
Total TN	283548
Total FP	526
Total FP CONTRA	58
Total FP INCONS	391
Total FP COMP	77
Total FN	794

Total Scores
MCC	0.536
Average MCC ± 95% Confidence Intervals	0.546 ± 0.080
Sensitivity	0.472
Positive Predictive Value	0.613
Nr of predictions	38

^top

2. Individual counts for Contrafold [ 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	13	5	3	5	7
2XQD_Y	tRNA links to Rfam database...	0.78	0.70	0.86	19	2828	3	0	3	0	8
3A2K_C	tRNA links to Rfam database...	0.44	0.43	0.46	12	2900	14	2	12	0	16
3AMU_B	tRNA links to Rfam database...	0.65	0.59	0.73	16	2981	8	0	6	2	11
3G4S_9	5S_rRNA links to Rfam database...	0.30	0.25	0.38	14	7344	23	1	22	0	43
3GX2_A	SAM links to Rfam database...	0.77	0.63	0.96	25	4345	2	0	1	1	15
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IZ4_A	tmRNA links to Rfam database...	0.52	0.45	0.61	60	70777	44	4	35	5	72
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.61	0.77	33	6860	10	1	9	0	21
3J20_0	tRNA links to Rfam database...	0.44	0.40	0.50	12	2826	13	0	12	1	18
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	4	0	0	4	2
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.49	0.65	26	7835	16	0	14	2	27
3J3D_C	tRNA links to Rfam database...	0.67	0.61	0.74	17	2752	6	0	6	0	11
3J3E_7	5S_rRNA links to Rfam database...	0.45	0.37	0.56	20	7104	16	1	15	0	34
3J3E_8	5_8S_rRNA links to Rfam database...	0.07	0.06	0.10	2	7483	32	1	17	14	31
3J3F_7	5S_rRNA links to Rfam database...	0.68	0.62	0.76	31	7219	11	0	10	1	19
3J3F_8	5_8S_rRNA links to Rfam database...	0.31	0.33	0.29	12	12205	41	4	25	12	24
3J3V_B	5S_rRNA links to Rfam database...	0.48	0.39	0.61	22	6985	14	1	13	0	35
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2830	20	0	20	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.20	0.21	0.20	7	12211	35	6	22	7	26
3JYX_3	5S_rRNA links to Rfam database...	0.28	0.30	0.27	8	6298	23	8	14	1	19
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...	0.76	0.70	0.84	32	6983	8	1	5	2	14
3O58_2	5S_rRNA links to Rfam database...	0.78	0.76	0.81	29	7224	10	2	5	3	9
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.26	0.31	9	12374	20	3	17	0	26
3PDR_A	ykoK links to Rfam database...	0.69	0.60	0.80	43	12826	13	0	11	2	29
3RKF_A	Purine links to Rfam database...	0.73	0.59	0.91	20	2189	2	1	1	0	14
3SD1_A	THF links to Rfam database...	0.57	0.48	0.69	20	3887	9	2	7	0	22
3ZEX_D	5S_rRNA links to Rfam database...	0.73	0.67	0.80	33	6980	8	1	7	0	16
3ZEX_C	5_8S_rRNA links to Rfam database...	0.28	0.21	0.38	11	14167	22	3	15	4	41
3ZND_W	tRNA links to Rfam database...	0.19	0.22	0.18	5	2975	25	1	22	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11751	33	5	20	8	28
4A1C_3	5S_rRNA links to Rfam database...	0.66	0.57	0.78	31	7100	9	1	8	0	23
4AOB_A	SAM links to Rfam database...	0.44	0.36	0.56	15	4344	13	1	11	1	27
4ENB_A	crcB links to Rfam database...	0.73	0.58	0.92	11	1263	1	1	0	0	8
4ENC_A	crcB links to Rfam database...	0.73	0.58	0.92	11	1314	1	1	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.68	0.56	0.82	18	3464	4	1	3	0	14

^top

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 Carnac(20) - scored higher in this pairwise comparison

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

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

Performance of Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

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