CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Carnac(20)		Vsfold4
MCC	0.598	>	0.459
Average MCC ± 95% Confidence Intervals	0.573 ± 0.073	>	0.497 ± 0.084
Sensitivity	0.398	>	0.381
Positive Predictive Value	0.902	>	0.558
Total TP	578	>	553
Total TN	269870	>	269520
Total FP	89	<	514
Total FP CONTRA	8	<	43
Total FP INCONS	55	<	395
Total FP COMP	26	<	76
Total FN	874	<	899
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Carnac(20) and Vsfold4. 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 Vsfold4).
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 Vsfold4).
Comparison of average Matthews Correlation Coefficients (MCCs) for Carnac(20) and Vsfold4. 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 Vsfold4).

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

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

Total Base Pair Counts
Total TP	578
Total TN	269870
Total FP	89
Total FP CONTRA	8
Total FP INCONS	55
Total FP COMP	26
Total FN	874

Total Scores
MCC	0.598
Average MCC ± 95% Confidence Intervals	0.573 ± 0.073
Sensitivity	0.398
Positive Predictive Value	0.902
Nr of predictions	37

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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_3	5S_rRNA links to Rfam database...	0.64	0.56	0.75	15	6308	10	1	4	5	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	12239	2	0	0	2	26
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
3ZND_W	tRNA links to Rfam database...	0.47	0.39	0.56	9	2987	10	0	7	3	14
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.15	0.71	5	11774	3	0	2	1	28
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

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Performance of Vsfold4 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold4

Total Base Pair Counts
Total TP	553
Total TN	269520
Total FP	514
Total FP CONTRA	43
Total FP INCONS	395
Total FP COMP	76
Total FN	899

Total Scores
MCC	0.459
Average MCC ± 95% Confidence Intervals	0.497 ± 0.084
Sensitivity	0.381
Positive Predictive Value	0.558
Nr of predictions	37

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2. Individual counts for Vsfold4 [ 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...	0.53	0.53	0.53	9	2833	12	5	3	4	8
2XQD_Y	tRNA links to Rfam database...	0.86	0.74	1.00	20	2830	0	0	0	0	7
3A2K_C	tRNA links to Rfam database...	0.84	0.71	1.00	20	2906	0	0	0	0	8
3AMU_B	tRNA links to Rfam database...	0.64	0.56	0.75	15	2983	7	0	5	2	12
3G4S_9	5S_rRNA links to Rfam database...	0.30	0.23	0.39	13	7348	20	1	19	0	44
3GX2_A	SAM links to Rfam database...	0.50	0.40	0.64	16	4346	10	0	9	1	24
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...	0.36	0.31	0.43	41	70780	59	7	48	4	91
3IZF_C	5S_rRNA links to Rfam database...	0.69	0.56	0.86	30	6868	5	0	5	0	24
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J20_1	tRNA links to Rfam database...	0.71	0.70	0.73	16	2904	6	0	6	0	7
3J2L_3	5S_rRNA links to Rfam database...	0.57	0.45	0.73	24	7842	12	1	8	3	29
3J3D_C	tRNA links to Rfam database...	0.44	0.39	0.50	11	2753	11	1	10	0	17
3J3E_7	5S_rRNA links to Rfam database...	0.48	0.35	0.66	19	7111	10	0	10	0	35
3J3E_8	5_8S_rRNA links to Rfam database...	0.07	0.06	0.09	2	7481	32	2	18	12	31
3J3F_7	5S_rRNA links to Rfam database...	0.21	0.18	0.26	9	7226	25	0	25	0	41
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.31	0.37	11	12216	27	4	15	8	25
3J3V_B	5S_rRNA links to Rfam database...	0.17	0.12	0.24	7	6992	22	1	21	0	50
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2831	19	0	19	0	32
3JYX_3	5S_rRNA links to Rfam database...	0.60	0.56	0.65	15	6305	11	4	4	3	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.10	0.09	0.12	3	12220	33	2	21	10	30
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...	0.61	0.50	0.74	23	6990	9	0	8	1	23
3O58_2	5S_rRNA links to Rfam database...	0.47	0.42	0.53	16	7230	16	3	11	2	22
3O58_3	5_8S_rRNA links to Rfam database...	0.09	0.09	0.10	3	12373	35	5	22	8	32
3PDR_A	ykoK links to Rfam database...	0.57	0.44	0.74	32	12837	13	0	11	2	40
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...	0.19	0.17	0.24	7	3887	22	1	21	0	35
3ZEX_D	5S_rRNA links to Rfam database...	0.55	0.45	0.69	22	6989	10	0	10	0	27
3ZND_W	tRNA links to Rfam database...	0.41	0.39	0.43	9	2982	14	2	10	2	14
4A1C_3	5S_rRNA links to Rfam database...	0.26	0.22	0.32	12	7103	25	2	23	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.28	0.24	0.33	8	11757	28	0	16	12	25
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1317	0	0	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.56	0.47	0.68	15	3464	7	1	6	0	17

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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 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 Vsfold4 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold4

2. Individual counts for Vsfold4 [ download as .csv ]