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	RNAshapes		Vsfold5
MCC	0.506	>	0.409
Average MCC ± 95% Confidence Intervals	0.508 ± 0.057	>	0.434 ± 0.066
Sensitivity	0.442	>	0.346
Positive Predictive Value	0.586	>	0.491
Total TP	1167	>	914
Total TN	457822	<	457952
Total FP	937	<	1035
Total FP CONTRA	91	<	103
Total FP INCONS	735	<	846
Total FP COMP	111	>	86
Total FN	1473	<	1726
P-value	3.56938820447e-08

^top

Performance plots

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

^top

Performance of RNAshapes - scored higher in this pairwise comparison

1. Total counts & total scores for RNAshapes

Total Base Pair Counts
Total TP	1167
Total TN	457822
Total FP	937
Total FP CONTRA	91
Total FP INCONS	735
Total FP COMP	111
Total FN	1473

Total Scores
MCC	0.506
Average MCC ± 95% Confidence Intervals	0.508 ± 0.057
Sensitivity	0.442
Positive Predictive Value	0.586
Nr of predictions	75

^top

2. Individual counts for RNAshapes [ 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...	0.91	0.83	1.00	15	846	0	0	0	0	3
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	1	0	0	1	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...	0.59	0.59	0.59	10	2833	12	4	3	5	7
2WW9_D	-	0.16	0.12	0.25	3	1941	9	4	5	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...	0.64	0.56	0.75	15	2830	5	0	5	0	12
2ZZM_B	tRNA links to Rfam database...	0.10	0.09	0.12	3	3460	23	0	23	0	29
2ZZN_D	tRNA links to Rfam database...	0.69	0.63	0.77	17	2463	5	1	4	0	10
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...	0.76	0.65	0.89	24	3628	3	0	3	0	13
3ADB_C	-	0.67	0.61	0.74	23	4155	8	0	8	0	15
3AKZ_H	tRNA links to Rfam database...	0.68	0.61	0.77	17	2679	6	1	4	1	11
3AM1_B	-	0.64	0.60	0.70	21	3210	9	1	8	0	14
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...	0.41	0.32	0.53	18	7347	16	1	15	0	39
3GCA_A	-	0.54	0.29	1.00	5	523	0	0	0	0	12
3GX2_A	SAM links to Rfam database...	0.76	0.63	0.93	25	4344	3	0	2	1	15
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...	0.76	0.67	0.88	22	4253	3	0	3	0	11
3IYQ_A	tmRNA links to Rfam database...	0.26	0.28	0.24	26	60619	83	21	60	2	68
3IZ4_A	tmRNA links to Rfam database...	0.52	0.45	0.60	60	70776	45	6	34	5	72
3IZF_C	5S_rRNA links to Rfam database...	0.59	0.52	0.68	28	6862	13	1	12	0	26
3J0L_2	-	0.38	0.36	0.40	12	6186	20	3	15	2	21
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	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...	0.50	0.40	0.63	12	2756	7	0	7	0	18
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	0	0	0	0	2
3J2C_O	-	0.39	0.33	0.47	21	10251	24	0	24	0	42
3J2L_3	5S_rRNA links to Rfam database...	0.59	0.51	0.69	27	7836	14	0	12	2	26
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...	0.48	0.41	0.58	22	7102	16	1	15	0	32
3J3E_8	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	7477	29	2	19	8	28
3J3F_7	5S_rRNA links to Rfam database...	0.68	0.58	0.81	29	7224	7	1	6	0	21
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.31	0.30	11	12209	39	3	23	13	25
3J3V_B	5S_rRNA links to Rfam database...	0.20	0.16	0.26	9	6987	25	0	25	0	48
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...	0.31	0.30	0.31	10	12214	35	5	17	13	23
3JYX_3	5S_rRNA links to Rfam database...	0.63	0.63	0.63	17	6301	21	1	9	11	10
3KTW_C	-	0.39	0.35	0.45	15	4527	19	1	17	1	28
3LA5_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2465	0	0	0	0	14
3NDB_M	-	0.82	0.72	0.94	44	9133	4	0	3	1	17
3NKB_B	-	0.61	0.54	0.70	14	1996	6	0	6	0	12
3NPB_A	SAM links to Rfam database...	0.77	0.63	0.94	29	6990	4	1	1	2	17
3O58_2	5S_rRNA links to Rfam database...	0.60	0.61	0.59	23	7221	18	4	12	2	15
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	37	2	21	14	23
3PDR_A	ykoK links to Rfam database...	0.67	0.56	0.80	40	12830	12	0	10	2	32
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...	0.39	0.32	0.48	12	3545	13	2	11	0	25
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.48	0.63	19	4723	12	1	10	1	21
3ZEX_E	-	0.00	0.00	0.00	0	21888	59	3	54	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.63	0.91	31	6987	3	0	3	0	18
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...	0.68	0.57	0.82	31	7102	7	1	6	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11746	41	5	25	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...	0.78	0.61	1.00	19	2831	0	0	0	0	12
4JRC_A	-	0.29	0.26	0.35	6	1523	11	0	11	0	17

^top

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

^top

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

^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 RNAshapes - scored higher in this pairwise comparison

1. Total counts & total scores for RNAshapes

2. Individual counts for RNAshapes [ 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 ]