CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CentroidFold		McQFold
MCC	0.483	>	0.373
Average MCC ± 95% Confidence Intervals	0.511 ± 0.058	>	0.481 ± 0.067
Sensitivity	0.397	>	0.293
Positive Predictive Value	0.587	>	0.476
Total TP	2496	>	1840
Total TN	11866016	<	11866405
Total FP	1922	<	2129
Total FP CONTRA	288	>	192
Total FP INCONS	1469	<	1832
Total FP COMP	165	>	105
Total FN	3789	<	4445
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of CentroidFold and McQFold. 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 CentroidFold and McQFold).
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 CentroidFold and McQFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidFold and McQFold. 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 CentroidFold and McQFold).

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Performance of CentroidFold - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidFold

Total Base Pair Counts
Total TP	2496
Total TN	11866016
Total FP	1922
Total FP CONTRA	288
Total FP INCONS	1469
Total FP COMP	165
Total FN	3789

Total Scores
MCC	0.483
Average MCC ± 95% Confidence Intervals	0.511 ± 0.058
Sensitivity	0.397
Positive Predictive Value	0.587
Nr of predictions	81

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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	-	0.42	0.26	0.71	5	623	2	0	2	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.49	0.35	0.70	7	1530	3	1	2	0	13
2LKR_A	-	0.82	0.74	0.91	29	6073	4	0	3	1	10
2M58_A	-	0.09	0.06	0.14	1	1646	6	0	6	0	16
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	12	5	3	4	7
2WW9_E	-	0.00	0.00	0.00	0	561	0	0	0	0	14
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WW9_D	-	0.29	0.12	0.75	3	1949	1	0	1	0	23
2WWQ_V	tRNA links to Rfam database...	0.80	0.68	0.95	19	2906	3	0	1	2	9
2XQD_Y	tRNA links to Rfam database...	0.75	0.67	0.86	18	2829	3	0	3	0	9
2ZZM_B	tRNA links to Rfam database...	0.18	0.16	0.23	5	3464	17	3	14	0	27
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...	0.44	0.43	0.46	12	2900	14	2	12	0	16
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
3ADB_C	-	0.92	0.84	1.00	32	4154	0	0	0	0	6
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
3GX2_A	SAM links to Rfam database...	0.79	0.63	1.00	25	4346	1	0	0	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...	0.80	0.67	0.96	22	4255	1	0	1	0	11
3IYQ_A	tmRNA links to Rfam database...	0.36	0.37	0.34	35	60624	71	17	50	4	59
3IZ4_A	tmRNA links to Rfam database...	0.55	0.45	0.68	59	70789	33	4	24	5	73
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.61	0.77	33	6860	10	1	9	0	21
3J0L_7	-	-0.01	0.00	0.00	0	1220	5	0	5	0	17
3J0L_2	-	0.25	0.24	0.28	8	6187	24	0	21	3	25
3J0L_g	-	0.00	0.00	0.00	0	465	0	0	0	0	4
3J0L_a	-	0.41	0.31	0.56	5	1119	4	2	2	0	11
3J16_L	tRNA links to Rfam database...	0.50	0.40	0.63	12	2756	7	0	7	0	18
3J20_1	tRNA links to Rfam database...	0.91	0.87	0.95	20	2905	2	0	1	1	3
3J20_0	tRNA links to Rfam database...	0.44	0.40	0.50	12	2826	13	0	12	1	18
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.56	0.48	0.67	303	1116310	158	8	144	6	330
3J2C_M	-	0.40	0.29	0.57	59	106387	47	5	40	2	148
3J2C_O	-	0.76	0.65	0.89	41	10250	6	0	5	1	22
3J2L_3	5S_rRNA links to Rfam database...	0.53	0.49	0.58	26	7830	21	0	19	2	27
3J3D_C	tRNA links to Rfam database...	0.49	0.43	0.57	12	2754	9	0	9	0	16
3J3E_7	5S_rRNA links to Rfam database...	0.46	0.37	0.59	20	7106	14	1	13	0	34
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7485	21	2	16	3	33
3J3F_7	5S_rRNA links to Rfam database...	0.20	0.18	0.23	9	7221	30	1	29	0	41
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.33	0.34	12	12211	34	4	19	11	24
3J3V_B	5S_rRNA links to Rfam database...	0.47	0.37	0.60	21	6986	14	1	13	0	36
3JYV_7	tRNA links to Rfam database...	0.77	0.59	1.00	19	2831	0	0	0	0	13
3JYX_3	5S_rRNA links to Rfam database...	0.29	0.30	0.30	8	6301	20	8	11	1	19
3JYX_5	-	0.36	0.33	0.40	294	5022122	510	149	300	61	599
3JYX_4	5_8S_rRNA links to Rfam database...	0.23	0.21	0.25	7	12218	25	5	16	4	26
3KIY_A	-	0.53	0.41	0.69	505	4053393	246	24	206	16	736
3KTW_C	-	0.45	0.40	0.53	17	4528	16	2	13	1	26
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.80	0.70	0.91	43	9133	5	0	4	1	18
3NKB_B	-	0.57	0.50	0.65	13	1996	7	0	7	0	13
3NPB_A	SAM links to Rfam database...	0.77	0.70	0.86	32	6984	7	1	4	2	14
3O58_2	5S_rRNA links to Rfam database...	0.82	0.76	0.88	29	7227	7	1	3	3	9
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.29	0.50	10	12383	10	0	10	0	25
3PDR_A	ykoK links to Rfam database...	0.73	0.60	0.90	43	12832	7	0	5	2	29
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...	0.58	0.48	0.71	20	3888	8	1	7	0	22
3U4M_B	-	0.57	0.46	0.71	17	3136	7	0	7	0	20
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
3W1K_J	tRNA-Sec links to Rfam database...	0.56	0.50	0.63	19	4156	11	2	9	0	19
3W3S_B	tRNA-Sec links to Rfam database...	0.87	0.78	0.97	31	4721	2	0	1	1	9
3ZEX_E	-	0.00	0.00	0.00	0	21895	52	3	47	2	77
3ZEX_G	-	0.36	0.28	0.46	21	16425	29	2	23	4	53
3ZEX_D	5S_rRNA links to Rfam database...	0.73	0.59	0.91	29	6989	3	0	3	0	20
3ZEX_B	-	0.23	0.16	0.34	87	1072121	178	9	163	6	471
3ZEX_H	-	0.19	0.18	0.21	7	9011	27	4	23	0	31
3ZEX_C	5_8S_rRNA links to Rfam database...	0.47	0.27	0.82	14	14179	3	1	2	0	38
3ZEX_F	-	0.00	0.00	0.00	0	2619	9	2	7	0	12
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11752	29	5	19	5	28
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.56	0.81	30	7103	7	1	6	0	24
4AOB_A	SAM links to Rfam database...	0.45	0.33	0.61	14	4348	10	1	8	1	28
4ATO_G	-	0.31	0.20	0.50	2	524	2	0	2	0	8
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...	0.73	0.58	0.92	11	1314	1	1	0	0	8
4FNJ_A	-	0.15	0.13	0.22	2	586	7	0	7	0	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.24	0.22	0.28	7	3461	18	3	15	0	25
4FRN_A	AdoCbl-variant links to Rfam database...	0.40	0.28	0.59	10	5134	7	2	5	0	26
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12
4JRC_A	-	0.81	0.70	0.94	16	1523	1	0	1	0	7

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Performance of McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

Total Base Pair Counts
Total TP	1840
Total TN	11866405
Total FP	2129
Total FP CONTRA	192
Total FP INCONS	1832
Total FP COMP	105
Total FN	4445

Total Scores
MCC	0.373
Average MCC ± 95% Confidence Intervals	0.481 ± 0.067
Sensitivity	0.293
Positive Predictive Value	0.476
Nr of predictions	81

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.59	0.53	0.68	21	5120	13	3	7	3	19
2KX8_A	7SK links to Rfam database...	0.88	0.83	0.94	15	845	1	0	1	0	3
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	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	-	0.51	0.46	0.58	18	6074	13	2	11	0	21
2M58_A	-	0.56	0.47	0.67	8	1641	4	1	3	0	9
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WW9_E	-	-0.01	0.00	0.00	0	556	5	0	5	0	14
2WW9_F	-	0.71	0.60	0.86	6	293	1	0	1	0	4
2WW9_D	-	0.32	0.23	0.46	6	1940	7	2	5	0	20
2WWQ_V	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	28
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	0.24	6	3461	19	2	17	0	26
2ZZN_D	tRNA links to Rfam database...	0.84	0.78	0.91	21	2462	2	0	2	0	6
3A2K_C	tRNA links to Rfam database...	0.86	0.75	1.00	21	2905	0	0	0	0	7
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
3ADB_C	-	0.92	0.84	1.00	32	4154	1	0	0	1	6
3AKZ_H	tRNA links to Rfam database...	0.68	0.61	0.77	17	2679	6	1	4	1	11
3AM1_B	-	0.91	0.83	1.00	29	3211	1	0	0	1	6
3AMU_B	tRNA links to Rfam database...	0.75	0.59	0.94	16	2986	3	0	1	2	11
3GX2_A	SAM links to Rfam database...	0.47	0.40	0.57	16	4343	13	1	11	1	24
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...	0.20	0.18	0.24	6	4253	19	2	17	0	27
3IYQ_A	tmRNA links to Rfam database...	0.28	0.31	0.26	29	60614	87	19	64	4	65
3IZ4_A	tmRNA links to Rfam database...	0.42	0.36	0.49	47	70780	53	6	43	4	85
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	6867	6	0	6	0	24
3J0L_7	-	-0.01	0.00	0.00	0	1215	10	0	10	0	17
3J0L_2	-	0.26	0.24	0.30	8	6189	21	0	19	2	25
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_a	-	0.26	0.19	0.38	3	1120	5	1	4	0	13
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.46	0.39	0.54	249	1116304	216	8	204	4	384
3J2C_M	-	0.31	0.25	0.38	51	106357	86	12	71	3	156
3J2C_O	-	0.53	0.43	0.66	27	10255	15	1	13	1	36
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.43	0.72	23	7843	11	0	9	2	30
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...	0.46	0.37	0.59	20	7106	14	1	13	0	34
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7479	36	3	21	12	33
3J3F_7	5S_rRNA links to Rfam database...	0.18	0.16	0.22	8	7223	29	1	28	0	42
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.31	0.30	11	12209	38	4	22	12	25
3J3V_B	5S_rRNA links to Rfam database...	0.49	0.33	0.73	19	6995	7	0	7	0	38
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2830	20	0	20	0	32
3JYX_3	5S_rRNA links to Rfam database...	0.21	0.22	0.20	6	6298	24	9	15	0	21
3JYX_5	-	0.00	0.00	0.00	0	5022865	0	0	0	0	893
3JYX_4	5_8S_rRNA links to Rfam database...	0.20	0.21	0.19	7	12210	33	8	21	4	26
3KIY_A	-	0.31	0.26	0.38	317	4053291	529	22	498	9	924
3KTW_C	-	0.36	0.30	0.45	13	4531	17	1	15	1	30
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.81	0.70	0.93	43	9134	4	1	2	1	18
3NKB_B	-	0.36	0.31	0.44	8	1998	10	1	9	0	18
3NPB_A	SAM links to Rfam database...	0.81	0.67	0.97	31	6989	4	1	0	3	15
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...	0.26	0.26	0.26	9	12368	26	10	16	0	26
3PDR_A	ykoK links to Rfam database...	0.69	0.56	0.87	40	12834	9	0	6	3	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...	0.71	0.60	0.86	25	3887	4	0	4	0	17
3U4M_B	-	0.73	0.57	0.95	21	3138	1	0	1	0	16
3UZL_B	tRNA links to Rfam database...	0.45	0.41	0.52	15	3541	14	0	14	0	22
3W1K_J	tRNA-Sec links to Rfam database...	0.78	0.63	0.96	24	4161	1	1	0	0	14
3W3S_B	tRNA-Sec links to Rfam database...	0.44	0.38	0.54	15	4725	14	0	13	1	25
3ZEX_E	-	0.00	0.00	0.00	0	21894	53	4	47	2	77
3ZEX_G	-	0.31	0.27	0.36	20	16416	38	1	34	3	54
3ZEX_D	5S_rRNA links to Rfam database...	0.69	0.53	0.90	26	6992	3	1	2	0	23
3ZEX_B	-	0.11	0.09	0.13	53	1071960	373	32	335	6	505
3ZEX_H	-	0.21	0.21	0.22	8	9009	29	6	22	1	30
3ZEX_C	5_8S_rRNA links to Rfam database...	0.27	0.21	0.34	11	14164	24	2	19	3	41
3ZEX_F	-	0.00	0.00	0.00	0	2619	9	2	7	0	12
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	33	5	23	5	28
4A1C_3	5S_rRNA links to Rfam database...	0.25	0.22	0.29	12	7099	29	1	28	0	42
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4ATO_G	-	-0.01	0.00	0.00	0	523	5	0	5	0	10
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
4FNJ_A	-	-0.02	0.00	0.00	0	588	7	0	7	0	16
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.66	1.00	21	3465	0	0	0	0	11
4FRN_A	AdoCbl-variant links to Rfam database...	0.73	0.56	0.95	20	5130	1	1	0	0	16
4JF2_A	preQ1-II links to Rfam database...	0.83	0.81	0.86	25	2821	4	3	1	0	6
4JRC_A	-	0.83	0.70	1.00	16	1524	0	0	0	0	7

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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 CentroidFold - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidFold

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

Performance of McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

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