CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Afold		McQFold
MCC	0.408	>	0.319
Average MCC ± 95% Confidence Intervals	0.476 ± 0.076	>	0.467 ± 0.087
Sensitivity	0.368	>	0.248
Positive Predictive Value	0.453	>	0.412
Total TP	2068	>	1392
Total TN	14427815	<	14428996
Total FP	2672	>	2052
Total FP CONTRA	352	>	175
Total FP INCONS	2141	>	1813
Total FP COMP	179	>	64
Total FN	3551	<	4227
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Afold - scored higher in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP	2068
Total TN	14427815
Total FP	2672
Total FP CONTRA	352
Total FP INCONS	2141
Total FP COMP	179
Total FN	3551

Total Scores
MCC	0.408
Average MCC ± 95% Confidence Intervals	0.476 ± 0.076
Sensitivity	0.368
Positive Predictive Value	0.453
Nr of predictions	54

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2. Individual counts for Afold [ 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	622	8	0	8	0	20
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	6	0	5	1	9
2LKR_A	-	0.93	0.87	1.00	34	6071	3	0	0	3	5
2M58_A	-	0.33	0.29	0.38	5	1640	8	1	7	0	12
2RP0_A	-	0.58	0.42	0.83	5	345	1	0	1	0	7
2WDL_A	-	0.43	0.37	0.50	447	3937333	444	31	410	3	757
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WW9_D	-	0.18	0.15	0.24	4	1936	13	0	13	0	22
2WW9_E	-	0.47	0.29	0.80	4	556	1	0	1	0	10
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...	0.80	0.74	0.87	20	2462	3	0	3	0	7
3A2K_C	tRNA links to Rfam database...	0.41	0.39	0.44	11	2901	14	2	12	0	17
3A3A_A	tRNA-Sec links to Rfam database...	0.84	0.70	1.00	26	3629	0	0	0	0	11
3ADB_C	-	0.78	0.74	0.82	28	4152	6	0	6	0	10
3AKZ_H	tRNA links to Rfam database...	0.16	0.14	0.19	4	2680	17	2	15	0	24
3AM1_B	-	0.72	0.66	0.79	23	3211	6	0	6	0	12
3G4S_9	5S_rRNA links to Rfam database...	0.48	0.35	0.67	20	7351	11	1	9	1	37
3GCA_A	-	-0.02	0.00	0.00	0	519	9	0	9	0	17
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...	0.62	0.58	0.68	19	4250	9	0	9	0	14
3IYQ_A	tmRNA links to Rfam database...	0.31	0.34	0.29	32	60616	82	23	55	4	62
3IZ4_A	tmRNA links to Rfam database...	0.48	0.45	0.51	59	70760	58	11	46	1	73
3IZF_C	5S_rRNA links to Rfam database...	0.66	0.57	0.76	31	6862	10	1	9	0	23
3J0L_7	-	-0.01	0.00	0.00	0	1210	15	1	14	0	17
3J2C_O	-	0.58	0.49	0.69	31	10251	15	1	13	1	32
3J3E_8	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	7477	31	2	19	10	28
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2827	23	1	22	0	32
3JYX_3	5S_rRNA links to Rfam database...	0.54	0.56	0.54	15	6300	24	1	12	11	12
3JYX_5	-	0.29	0.30	0.29	268	5021928	735	179	490	66	625
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.31	10	12214	35	5	17	13	23
3KIY_A	-	0.43	0.36	0.50	449	4053235	456	24	420	12	792
3KTW_C	-	0.71	0.63	0.82	27	4527	7	2	4	1	16
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.84	0.74	0.96	45	9133	3	0	2	1	16
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NPB_A	SAM links to Rfam database...	0.74	0.61	0.90	28	6990	5	0	3	2	18
3O58_2	5S_rRNA links to Rfam database...	0.66	0.66	0.66	25	7222	14	4	9	1	13
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	37	2	21	14	23
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3W3S_B	tRNA-Sec links to Rfam database...	0.50	0.45	0.56	18	4721	15	1	13	1	22
3ZEX_B	-	0.29	0.26	0.32	147	1071922	322	35	276	11	411
3ZEX_F	-	0.00	0.00	0.00	0	2617	12	2	9	1	12
3ZEX_D	5S_rRNA links to Rfam database...	0.72	0.61	0.86	30	6986	5	0	5	0	19
3ZEX_H	-	0.18	0.18	0.18	7	9006	33	6	26	1	31
3ZEX_E	-	0.00	0.00	0.00	0	21892	55	2	51	2	77
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	43	5	26	12	28
4ATO_G	-	0.32	0.30	0.38	3	520	6	1	4	1	7
4ENB_A	crcB links to Rfam database...	0.67	0.58	0.79	11	1261	3	1	2	0	8
4FNJ_A	-	0.75	0.63	0.91	10	584	1	0	1	0	6
4JRC_A	-	0.24	0.22	0.29	5	1523	12	0	12	0	18

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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	1392
Total TN	14428996
Total FP	2052
Total FP CONTRA	175
Total FP INCONS	1813
Total FP COMP	64
Total FN	4227

Total Scores
MCC	0.319
Average MCC ± 95% Confidence Intervals	0.467 ± 0.087
Sensitivity	0.248
Positive Predictive Value	0.412
Nr of predictions	54

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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
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KFC_A	-	0.49	0.25	1.00	5	625	0	0	0	0	15
2KX8_A	7SK links to Rfam database...	0.88	0.83	0.94	15	845	1	0	1	0	3
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
2RP0_A	-	0.64	0.42	1.00	5	346	0	0	0	0	7
2WDL_A	-	0.31	0.26	0.37	308	3937383	531	27	503	1	896
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
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
2WW9_E	-	-0.01	0.00	0.00	0	556	5	0	5	0	14
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
3G4S_9	5S_rRNA links to Rfam database...	0.27	0.21	0.36	12	7348	21	1	20	0	45
3GCA_A	-	0.54	0.29	1.00	5	523	0	0	0	0	12
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
3J2C_O	-	0.53	0.43	0.66	27	10255	15	1	13	1	36
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7479	36	3	21	12	33
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
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3U4M_B	-	0.73	0.57	0.95	21	3138	1	0	1	0	16
3W3S_B	tRNA-Sec links to Rfam database...	0.44	0.38	0.54	15	4725	14	0	13	1	25
3ZEX_B	-	0.11	0.09	0.13	53	1071960	373	32	335	6	505
3ZEX_F	-	0.00	0.00	0.00	0	2619	9	2	7	0	12
3ZEX_D	5S_rRNA links to Rfam database...	0.69	0.53	0.90	26	6992	3	1	2	0	23
3ZEX_H	-	0.21	0.21	0.22	8	9009	29	6	22	1	30
3ZEX_E	-	0.00	0.00	0.00	0	21894	53	4	47	2	77
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	33	5	23	5	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
4FNJ_A	-	-0.02	0.00	0.00	0	588	7	0	7	0	16
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 Afold - scored higher in this pairwise comparison

1. Total counts & total scores for Afold

2. Individual counts for Afold [ 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 ]