CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ProbKnot		Vsfold4
MCC	0.535	>	0.433
Average MCC ± 95% Confidence Intervals	0.516 ± 0.076	>	0.455 ± 0.068
Sensitivity	0.481	>	0.360
Positive Predictive Value	0.600	>	0.526
Total TP	976	>	731
Total TN	395420	<	395656
Total FP	745	>	730
Total FP CONTRA	86	>	59
Total FP INCONS	565	<	601
Total FP COMP	94	>	70
Total FN	1055	<	1300
P-value	3.56938820447e-08

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Performance plots

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

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Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	976
Total TN	395420
Total FP	745
Total FP CONTRA	86
Total FP INCONS	565
Total FP COMP	94
Total FN	1055

Total Scores
MCC	0.535
Average MCC ± 95% Confidence Intervals	0.516 ± 0.076
Sensitivity	0.481
Positive Predictive Value	0.600
Nr of predictions	52

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.69	0.60	0.80	24	5121	11	2	4	5	16
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LA5_A	-	0.45	0.32	0.67	6	621	3	0	3	0	13
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2LKR_A	-	0.85	0.77	0.94	30	6073	4	0	2	2	9
2M58_A	-	-0.01	0.00	0.00	0	1638	15	0	15	0	17
2XQD_Y	tRNA links to Rfam database...	0.90	0.81	1.00	22	2828	1	0	0	1	5
3AKZ_H	tRNA links to Rfam database...	0.73	0.75	0.72	21	2672	8	4	4	0	7
3AM1_B	-	0.74	0.71	0.78	25	3208	7	1	6	0	10
3AMU_B	tRNA links to Rfam database...	0.65	0.59	0.73	16	2981	8	0	6	2	11
3IYQ_A	tmRNA links to Rfam database...	0.28	0.31	0.26	29	60616	85	22	59	4	65
3IZ4_A	tmRNA links to Rfam database...	0.52	0.46	0.60	61	70774	46	6	35	5	71
3IZF_C	5S_rRNA links to Rfam database...	0.72	0.61	0.85	33	6864	6	0	6	0	21
3J0L_2	-	0.27	0.27	0.28	9	6184	26	2	21	3	24
3J0L_a	-	0.55	0.50	0.62	8	1115	5	2	3	0	8
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_g	-	-0.01	0.00	0.00	0	458	7	2	5	0	4
3J16_L	tRNA links to Rfam database...	0.35	0.33	0.38	10	2749	16	1	15	0	20
3J20_1	tRNA links to Rfam database...	0.71	0.70	0.73	16	2904	7	0	6	1	7
3J20_0	tRNA links to Rfam database...	0.45	0.40	0.52	12	2827	12	0	11	1	18
3J2C_O	-	0.60	0.52	0.70	33	10249	15	0	14	1	30
3J2L_3	5S_rRNA links to Rfam database...	0.60	0.49	0.74	26	7840	11	0	9	2	27
3J3D_C	tRNA links to Rfam database...	0.46	0.43	0.50	12	2751	12	1	11	0	16
3J3E_7	5S_rRNA links to Rfam database...	0.47	0.35	0.63	19	7110	11	0	11	0	35
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7476	37	3	24	10	33
3J3F_7	5S_rRNA links to Rfam database...	0.76	0.64	0.91	32	7225	3	0	3	0	18
3J3F_8	5_8S_rRNA links to Rfam database...	0.35	0.33	0.36	12	12213	35	3	18	14	24
3J3V_B	5S_rRNA links to Rfam database...	0.53	0.42	0.67	24	6985	12	1	11	0	33
3NDB_M	-	0.77	0.69	0.88	42	9132	7	0	6	1	19
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NPB_A	SAM links to Rfam database...	0.72	0.61	0.85	28	6988	8	1	4	3	18
3O58_2	5S_rRNA links to Rfam database...	0.76	0.76	0.76	29	7222	10	3	6	1	9
3O58_3	5_8S_rRNA links to Rfam database...	0.31	0.34	0.29	12	12362	41	4	25	12	23
3PDR_A	ykoK links to Rfam database...	0.74	0.64	0.85	46	12826	10	1	7	2	26
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...	0.55	0.48	0.65	20	3885	11	2	9	0	22
3U4M_B	-	0.45	0.35	0.59	13	3138	9	1	8	0	24
3UZL_B	tRNA links to Rfam database...	0.73	0.62	0.85	23	3543	4	0	4	0	14
3W3S_B	tRNA-Sec links to Rfam database...	0.89	0.80	1.00	32	4721	1	0	0	1	8
3ZEX_D	5S_rRNA links to Rfam database...	0.77	0.67	0.89	33	6984	4	0	4	0	16
3ZEX_E	-	0.00	0.00	0.00	0	21886	61	2	57	2	77
3ZEX_G	-	0.77	0.66	0.91	49	16417	10	0	5	5	25
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	24	1	20	3	18
4A1C_3	5S_rRNA links to Rfam database...	0.73	0.61	0.87	33	7102	6	1	4	1	21
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.12	5	11738	49	7	31	11	28
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ATO_G	-	0.32	0.30	0.38	3	520	5	1	4	0	7
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...	0.45	0.42	0.50	8	1310	8	1	7	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.37	0.31	0.45	10	3464	12	3	9	0	22
4JF2_A	preQ1-II links to Rfam database...	0.80	0.71	0.92	22	2826	2	2	0	0	9
4JRC_A	-	0.25	0.22	0.31	5	1524	11	0	11	0	18

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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	731
Total TN	395656
Total FP	730
Total FP CONTRA	59
Total FP INCONS	601
Total FP COMP	70
Total FN	1300

Total Scores
MCC	0.433
Average MCC ± 95% Confidence Intervals	0.455 ± 0.068
Sensitivity	0.360
Positive Predictive Value	0.526
Nr of predictions	52

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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
2KRL_A	-	0.65	0.53	0.81	21	5125	7	0	5	2	19
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1527	13	0	13	0	20
2LKR_A	-	0.31	0.28	0.34	11	6073	21	3	18	0	28
2M58_A	-	-0.01	0.00	0.00	0	1647	6	0	6	0	17
2XQD_Y	tRNA links to Rfam database...	0.86	0.74	1.00	20	2830	0	0	0	0	7
3AKZ_H	tRNA links to Rfam database...	0.67	0.57	0.80	16	2681	5	1	3	1	12
3AM1_B	-	0.84	0.71	1.00	25	3215	0	0	0	0	10
3AMU_B	tRNA links to Rfam database...	0.64	0.56	0.75	15	2983	7	0	5	2	12
3IYQ_A	tmRNA links to Rfam database...	0.29	0.29	0.29	27	60634	71	13	52	6	67
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
3J0L_2	-	0.38	0.36	0.41	12	6187	18	3	14	1	21
3J0L_a	-	0.39	0.31	0.50	5	1118	5	2	3	0	11
3J0L_7	-	0.51	0.41	0.64	7	1214	4	0	4	0	10
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J16_L	tRNA links to Rfam database...	0.82	0.67	1.00	20	2755	0	0	0	0	10
3J20_1	tRNA links to Rfam database...	0.71	0.70	0.73	16	2904	6	0	6	0	7
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J2C_O	-	0.30	0.24	0.39	15	10258	24	0	23	1	48
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
3NDB_M	-	0.28	0.23	0.35	14	9140	26	0	26	0	47
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
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
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.53	0.41	0.71	15	3549	6	1	5	0	22
3W3S_B	tRNA-Sec links to Rfam database...	0.67	0.58	0.79	23	4724	7	0	6	1	17
3ZEX_D	5S_rRNA links to Rfam database...	0.55	0.45	0.69	22	6989	10	0	10	0	27
3ZEX_E	-	0.08	0.06	0.11	5	21900	40	1	39	0	72
3ZEX_G	-	0.30	0.23	0.39	17	16427	27	2	25	0	57
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
4ATO_G	-	0.32	0.30	0.38	3	520	5	1	4	0	7
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
4JF2_A	preQ1-II links to Rfam database...	0.66	0.52	0.84	16	2831	3	0	3	0	15
4JRC_A	-	0.29	0.22	0.42	5	1528	7	0	7	0	18

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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 ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

2. Individual counts for ProbKnot [ 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 ]