CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAfold		Vsfold5
MCC	0.528	>	0.409
Average MCC ± 95% Confidence Intervals	0.522 ± 0.059	>	0.434 ± 0.066
Sensitivity	0.466	>	0.346
Positive Predictive Value	0.605	>	0.491
Total TP	1230	>	914
Total TN	457781	<	457952
Total FP	916	<	1035
Total FP CONTRA	97	<	103
Total FP INCONS	707	<	846
Total FP COMP	112	>	86
Total FN	1410	<	1726
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of RNAfold and Vsfold5. 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 RNAfold and Vsfold5).
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 RNAfold and Vsfold5).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAfold and Vsfold5. 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 RNAfold and Vsfold5).

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Performance of RNAfold - scored higher in this pairwise comparison

1. Total counts & total scores for RNAfold

Total Base Pair Counts
Total TP	1230
Total TN	457781
Total FP	916
Total FP CONTRA	97
Total FP INCONS	707
Total FP COMP	112
Total FN	1410

Total Scores
MCC	0.528
Average MCC ± 95% Confidence Intervals	0.522 ± 0.059
Sensitivity	0.466
Positive Predictive Value	0.605
Nr of predictions	75

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2. Individual counts for RNAfold [ 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
2KFC_A	-	-0.02	0.00	0.00	0	623	7	0	7	0	20
2KRL_A	-	0.76	0.60	0.96	24	5126	5	0	1	4	16
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LA5_A	-	0.39	0.26	0.63	5	622	3	1	2	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2LKR_A	-	0.93	0.87	1.00	34	6071	3	0	0	3	5
2M58_A	-	0.34	0.29	0.42	5	1641	7	1	6	0	12
2RP0_A	-	0.64	0.42	1.00	5	346	0	0	0	0	7
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WW9_D	-	0.14	0.12	0.19	3	1937	13	0	13	0	23
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WW9_E	-	0.53	0.29	1.00	4	557	0	0	0	0	10
2WWQ_V	tRNA links to Rfam database...	0.76	0.68	0.86	19	2904	5	0	3	2	9
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2ZZM_B	tRNA links to Rfam database...	0.21	0.19	0.25	6	3462	18	0	18	0	26
2ZZN_D	tRNA links to Rfam database...	0.82	0.78	0.88	21	2461	3	0	3	0	6
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
3ADB_C	-	0.33	0.32	0.35	12	4152	22	0	22	0	26
3AKZ_H	tRNA links to Rfam database...	0.43	0.39	0.48	11	2678	12	2	10	0	17
3AM1_B	-	0.68	0.63	0.73	22	3210	8	1	7	0	13
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3G4S_9	5S_rRNA links to Rfam database...	0.51	0.39	0.69	22	7349	10	1	9	0	35
3GCA_A	-	0.54	0.29	1.00	5	523	0	0	0	0	12
3GX2_A	SAM links to Rfam database...	0.68	0.55	0.85	22	4345	5	0	4	1	18
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.63	0.58	0.70	19	4251	9	0	8	1	14
3IYQ_A	tmRNA links to Rfam database...	0.31	0.34	0.29	32	60616	80	24	54	2	62
3IZ4_A	tmRNA links to Rfam database...	0.51	0.47	0.55	62	70763	52	10	41	1	70
3IZF_C	5S_rRNA links to Rfam database...	0.59	0.52	0.67	28	6861	14	1	13	0	26
3J0L_2	-	0.25	0.24	0.26	8	6185	25	2	21	2	25
3J0L_g	-	-0.01	0.00	0.00	0	460	5	1	4	0	4
3J0L_a	-	0.23	0.19	0.30	3	1118	7	1	6	0	13
3J0L_7	-	-0.01	0.00	0.00	0	1213	12	0	12	0	17
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_0	tRNA links to Rfam database...	0.43	0.40	0.48	12	2825	14	0	13	1	18
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	2	0	0	2	2
3J2C_O	-	0.64	0.54	0.76	34	10251	12	0	11	1	29
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.53	0.74	28	7837	12	0	10	2	25
3J3D_C	tRNA links to Rfam database...	0.28	0.25	0.32	7	2753	15	1	14	0	21
3J3E_7	5S_rRNA links to Rfam database...	0.58	0.48	0.70	26	7103	11	1	10	0	28
3J3E_8	5_8S_rRNA links to Rfam database...	0.16	0.15	0.19	5	7476	31	2	20	9	28
3J3F_7	5S_rRNA links to Rfam database...	0.73	0.64	0.84	32	7222	7	0	6	1	18
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.31	0.31	11	12210	39	4	21	14	25
3J3V_B	5S_rRNA links to Rfam database...	0.54	0.44	0.68	25	6984	12	1	11	0	32
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2828	22	1	21	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.32	10	12215	33	5	16	12	23
3JYX_3	5S_rRNA links to Rfam database...	0.62	0.63	0.61	17	6300	22	1	10	11	10
3KTW_C	-	0.73	0.63	0.84	27	4528	6	2	3	1	16
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.77	0.69	0.86	42	9131	8	0	7	1	19
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NPB_A	SAM links to Rfam database...	0.83	0.72	0.97	33	6987	4	0	1	3	13
3O58_2	5S_rRNA links to Rfam database...	0.59	0.61	0.58	23	7220	19	4	13	2	15
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	34	2	21	11	23
3PDR_A	ykoK links to Rfam database...	0.75	0.63	0.90	45	12830	7	1	4	2	27
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...	0.64	0.52	0.79	22	3888	6	1	5	0	20
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.48	0.38	0.61	14	3547	9	0	9	0	23
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.50	0.61	20	4720	14	1	12	1	20
3ZEX_E	-	0.00	0.00	0.00	0	21893	54	4	48	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.77	0.65	0.91	32	6986	3	0	3	0	17
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	22	1	20	1	18
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11744	43	5	27	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...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1314	7	1	6	0	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.32	0.28	0.38	9	3462	15	0	15	0	23
4FRN_A	AdoCbl-variant links to Rfam database...	0.52	0.44	0.62	16	5125	10	2	8	0	20
4JF2_A	preQ1-II links to Rfam database...	0.76	0.61	0.95	19	2830	1	0	1	0	12
4JRC_A	-	0.29	0.26	0.35	6	1523	11	0	11	0	17

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Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

Total Base Pair Counts
Total TP	914
Total TN	457952
Total FP	1035
Total FP CONTRA	103
Total FP INCONS	846
Total FP COMP	86
Total FN	1726

Total Scores
MCC	0.409
Average MCC ± 95% Confidence Intervals	0.434 ± 0.066
Sensitivity	0.346
Positive Predictive Value	0.491
Nr of predictions	75

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2. Individual counts for Vsfold5 [ 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...	0.90	0.82	1.00	9	397	0	0	0	0	2
2KFC_A	-	0.48	0.35	0.70	7	620	3	0	3	0	13
2KRL_A	-	0.57	0.50	0.65	20	5120	11	5	6	0	20
2KX8_A	7SK links to Rfam database...	0.91	0.83	1.00	15	846	0	0	0	0	3
2LA5_A	-	-0.02	0.00	0.00	0	623	7	0	7	0	19
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1527	13	0	13	0	20
2LKR_A	-	0.27	0.23	0.32	9	6077	19	2	17	0	30
2M58_A	-	0.32	0.24	0.44	4	1644	5	1	4	0	13
2RP0_A	-	0.64	0.42	1.00	5	346	0	0	0	0	7
2WRQ_Y	tRNA links to Rfam database...	0.53	0.53	0.53	9	2833	12	5	3	4	8
2WW9_D	-	0.15	0.12	0.21	3	1939	11	1	10	0	23
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WW9_E	-	-0.01	0.00	0.00	0	556	5	0	5	0	14
2WWQ_V	tRNA links to Rfam database...	0.64	0.50	0.82	14	2909	4	0	3	1	14
2XQD_Y	tRNA links to Rfam database...	0.86	0.74	1.00	20	2830	0	0	0	0	7
2ZZM_B	tRNA links to Rfam database...	0.19	0.19	0.21	6	3458	22	1	21	0	26
2ZZN_D	tRNA links to Rfam database...	0.86	0.78	0.95	21	2463	1	0	1	0	6
3A2K_C	tRNA links to Rfam database...	0.84	0.71	1.00	20	2906	0	0	0	0	8
3A3A_A	tRNA-Sec links to Rfam database...	0.85	0.73	1.00	27	3628	0	0	0	0	10
3ADB_C	-	0.67	0.53	0.87	20	4163	3	0	3	0	18
3AKZ_H	tRNA links to Rfam database...	0.84	0.71	1.00	20	2681	0	0	0	0	8
3AM1_B	-	0.78	0.71	0.86	25	3211	4	1	3	0	10
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3G4S_9	5S_rRNA links to Rfam database...	0.08	0.07	0.11	4	7344	33	0	33	0	53
3GCA_A	-	0.54	0.29	1.00	5	523	0	0	0	0	12
3GX2_A	SAM links to Rfam database...	0.51	0.40	0.67	16	4347	9	0	8	1	24
3IVN_B	Purine links to Rfam database...	0.76	0.58	1.00	18	2328	0	0	0	0	13
3IWN_A	c-di-GMP-I links to Rfam database...	0.25	0.21	0.30	7	4255	16	1	15	0	26
3IYQ_A	tmRNA links to Rfam database...	0.33	0.31	0.35	29	60642	61	15	40	6	65
3IZ4_A	tmRNA links to Rfam database...	0.29	0.24	0.36	32	70787	62	8	49	5	100
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.56	0.88	30	6869	4	0	4	0	24
3J0L_2	-	0.35	0.33	0.37	11	6186	21	3	16	2	22
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_a	-	0.39	0.31	0.50	5	1118	5	2	3	0	11
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J16_L	tRNA links to Rfam database...	0.82	0.67	1.00	20	2755	0	0	0	0	10
3J20_0	tRNA links to Rfam database...	0.67	0.57	0.81	17	2829	5	1	3	1	13
3J20_1	tRNA links to Rfam database...	0.71	0.70	0.73	16	2904	6	0	6	0	7
3J2C_O	-	0.30	0.24	0.39	15	10258	24	0	23	1	48
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.45	0.71	24	7841	13	1	9	3	29
3J3D_C	tRNA links to Rfam database...	0.60	0.54	0.68	15	2753	7	0	7	0	13
3J3E_7	5S_rRNA links to Rfam database...	0.47	0.37	0.61	20	7107	13	0	13	0	34
3J3E_8	5_8S_rRNA links to Rfam database...	0.06	0.06	0.08	2	7477	31	5	19	7	31
3J3F_7	5S_rRNA links to Rfam database...	0.21	0.18	0.26	9	7226	25	1	24	0	41
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.33	0.33	12	12210	35	5	19	11	24
3J3V_B	5S_rRNA links to Rfam database...	0.16	0.12	0.21	7	6988	26	1	25	0	50
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2831	19	0	19	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.31	10	12214	32	3	19	10	23
3JYX_3	5S_rRNA links to Rfam database...	0.17	0.15	0.20	4	6308	18	4	12	2	23
3KTW_C	-	0.38	0.30	0.50	13	4534	13	3	10	0	30
3LA5_A	Purine links to Rfam database...	-0.01	0.00	0.00	0	2469	16	0	16	0	34
3NDB_M	-	0.06	0.05	0.08	3	9144	33	1	32	0	58
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NPB_A	SAM links to Rfam database...	0.57	0.46	0.72	21	6992	9	1	7	1	25
3O58_2	5S_rRNA links to Rfam database...	0.45	0.42	0.48	16	7227	19	3	14	2	22
3O58_3	5_8S_rRNA links to Rfam database...	0.39	0.37	0.41	13	12371	28	7	12	9	22
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...	0.75	0.65	0.88	22	2186	3	0	3	0	12
3SD1_A	THF links to Rfam database...	0.11	0.10	0.15	4	3890	22	0	22	0	38
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.16	0.14	0.20	5	3545	20	1	19	0	32
3W3S_B	tRNA-Sec links to Rfam database...	0.76	0.70	0.82	28	4719	7	1	5	1	12
3ZEX_E	-	0.07	0.06	0.08	5	21886	54	5	49	0	72
3ZEX_D	5S_rRNA links to Rfam database...	0.08	0.06	0.11	3	6994	24	0	24	0	46
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...	0.24	0.24	0.24	8	11748	37	3	22	12	25
4AOB_A	SAM links to Rfam database...	0.18	0.14	0.25	6	4347	19	1	17	1	36
4ATO_G	-	0.56	0.60	0.55	6	517	5	1	4	0	4
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.56	0.47	0.68	15	3464	7	1	6	0	17
4FRN_A	AdoCbl-variant links to Rfam database...	0.13	0.11	0.17	4	5128	19	2	17	0	32
4JF2_A	preQ1-II links to Rfam database...	0.84	0.77	0.92	24	2824	2	1	1	0	7
4JRC_A	-	0.25	0.22	0.31	5	1524	11	0	11	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 RNAfold - scored higher in this pairwise comparison

1. Total counts & total scores for RNAfold

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

Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

2. Individual counts for Vsfold5 [ download as .csv ]