CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Fold		Afold
MCC	0.652	>	0.630
Average MCC ± 95% Confidence Intervals	0.775 ± 0.083	>	0.762 ± 0.079
Sensitivity	0.689	>	0.669
Positive Predictive Value	0.618	>	0.596
Total TP	1141	>	1108
Total TN	538428	>	538414
Total FP	873	<	929
Total FP CONTRA	238	<	241
Total FP INCONS	466	<	510
Total FP COMP	169	<	178
Total FN	515	<	548
P-value	4.1569883686e-08

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Performance plots

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

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Performance of Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

Total Base Pair Counts
Total TP	1141
Total TN	538428
Total FP	873
Total FP CONTRA	238
Total FP INCONS	466
Total FP COMP	169
Total FN	515

Total Scores
MCC	0.652
Average MCC ± 95% Confidence Intervals	0.775 ± 0.083
Sensitivity	0.689
Positive Predictive Value	0.618
Nr of predictions	67

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KPV_A	-	0.96	0.92	1.00	12	201	0	0	0	0	1
2KU0_A	-	0.96	0.92	1.00	11	281	0	0	0	0	1
2KUR_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	448	0	0	0	0	0
2KUU_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	429	1	0	0	1	0
2KUV_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	420	0	0	0	0	0
2KUW_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	452	1	0	0	1	0
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2KXM_A	-	0.93	0.88	1.00	7	142	0	0	0	0	1
2KZL_A	-	1.00	1.00	1.00	13	507	1	0	0	1	0
2L1F_B	Gammaretro_CES links to Rfam database...	0.91	0.92	0.92	22	767	2	0	2	0	2
2L1F_A	Gammaretro_CES links to Rfam database...	0.91	0.91	0.91	21	740	2	0	2	0	2
2L2K_A	-	1.00	1.00	1.00	17	332	0	0	0	0	0
2L3C_B	-	1.00	1.00	1.00	14	225	0	0	0	0	0
2L3E_A	-	1.00	1.00	1.00	12	228	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	1.00	1.00	1.00	30	955	0	0	0	0	0
2L5Z_A	-	1.00	1.00	1.00	9	102	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.90	0.90	0.90	26	2411	10	0	3	7	3
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	1.00	1.00	1.00	11	196	1	0	0	1	0
2XXA_G	Bacteria_small_SRP links to Rfam database...	1.00	1.00	1.00	35	2010	1	0	0	1	0
2YIE_X	-	0.39	0.43	0.38	3	536	8	1	4	3	4
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
3ADB_C	-	0.86	0.85	0.88	28	1787	4	0	4	0	5
3AKZ_H	tRNA links to Rfam database...	1.00	1.00	1.00	20	1107	2	0	0	2	0
3AM1_B	-	0.86	0.86	0.86	25	1437	4	0	4	0	4
3IYQ_A	tmRNA links to Rfam database...	0.24	0.33	0.18	17	22345	95	40	38	17	34
3IZ4_A	tmRNA links to Rfam database...	0.60	0.61	0.59	58	25437	47	16	25	6	37
3IZF_C	5S_rRNA links to Rfam database...	0.87	0.89	0.86	31	2604	8	0	5	3	4
3J0L_7	-	-0.02	0.00	0.00	0	507	12	2	10	0	10
3J0L_1	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_h	-	0.93	0.88	1.00	28	2112	2	0	0	2	4
3J2C_O	-	0.71	0.76	0.67	31	3941	21	5	10	6	10
3NDB_M	-	1.00	1.00	1.00	44	3670	4	0	0	4	0
3NKB_B	-	0.41	0.42	0.42	8	716	11	4	7	0	11
3NMU_E	-	-0.02	0.00	0.00	0	207	11	6	3	2	3
3NPB_A	SAM links to Rfam database...	0.77	0.73	0.82	27	2245	11	0	6	5	10
3O58_3	5_8S_rRNA links to Rfam database...	0.39	0.50	0.31	11	4728	41	9	16	16	11
3O58_2	5S_rRNA links to Rfam database...	0.86	0.87	0.84	27	2722	12	0	5	7	4
3OVS_D	-	1.00	1.00	1.00	12	204	0	0	0	0	0
3P22_G	-	1.00	1.00	1.00	11	301	0	0	0	0	0
3R4F_A	-	1.00	1.00	1.00	22	884	1	0	0	1	0
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SIU_F	-	1.00	1.00	1.00	8	137	0	0	0	0	0
3SN2_B	IRE_II links to Rfam database...	1.00	1.00	1.00	12	142	0	0	0	0	0
3U4M_B	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.94	0.91	0.97	30	1958	2	0	1	1	3
3ZEX_H	-	0.26	0.37	0.19	7	3588	30	19	11	0	12
3ZEX_E	-	-0.01	0.00	0.00	0	8249	57	20	35	2	34
3ZEX_D	5S_rRNA links to Rfam database...	0.90	0.86	0.94	30	2764	8	0	2	6	5
3ZEX_B	-	0.32	0.36	0.29	123	420926	346	87	216	43	223
3ZEX_F	-	-0.01	0.00	0.00	0	908	11	2	4	5	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4482	43	11	18	14	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4ATO_G	-	0.38	0.43	0.38	3	212	5	5	0	0	4
4ENB_A	crcB links to Rfam database...	0.37	0.33	0.45	5	461	7	0	6	1	10
4FNJ_A	-	0.91	0.83	1.00	10	240	0	0	0	0	2
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

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Performance of Afold - scored lower in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP	1108
Total TN	538414
Total FP	929
Total FP CONTRA	241
Total FP INCONS	510
Total FP COMP	178
Total FN	548

Total Scores
MCC	0.630
Average MCC ± 95% Confidence Intervals	0.762 ± 0.079
Sensitivity	0.669
Positive Predictive Value	0.596
Nr of predictions	67

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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
2KPV_A	-	0.96	0.92	1.00	12	201	0	0	0	0	1
2KU0_A	-	1.00	1.00	1.00	12	280	0	0	0	0	0
2KUR_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	448	0	0	0	0	0
2KUU_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	429	1	0	0	1	0
2KUV_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	420	0	0	0	0	0
2KUW_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	452	1	0	0	1	0
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2KXM_A	-	1.00	1.00	1.00	8	141	0	0	0	0	0
2KZL_A	-	1.00	1.00	1.00	13	507	1	0	0	1	0
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	1.00	0.96	24	766	1	0	1	0	0
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	1.00	0.96	23	739	1	0	1	0	0
2L2K_A	-	1.00	1.00	1.00	17	332	0	0	0	0	0
2L3C_B	-	1.00	1.00	1.00	14	225	0	0	0	0	0
2L3E_A	-	1.00	1.00	1.00	12	228	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	1.00	1.00	1.00	30	955	0	0	0	0	0
2L5Z_A	-	1.00	1.00	1.00	9	102	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	6	0	5	1	7
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	1.00	1.00	1.00	29	2411	8	0	0	8	0
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.85	0.82	0.90	9	197	2	0	1	1	2
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.35	0.34	0.38	12	2013	21	1	19	1	23
2YIE_X	-	0.53	0.57	0.50	4	536	8	1	3	4	3
2YIE_Z	-	-0.02	0.00	0.00	0	587	16	6	9	1	8
3ADB_C	-	0.85	0.85	0.85	28	1786	6	0	5	1	5
3AKZ_H	tRNA links to Rfam database...	0.19	0.20	0.21	4	1108	17	4	11	2	16
3AM1_B	-	0.79	0.79	0.79	23	1437	6	0	6	0	6
3IYQ_A	tmRNA links to Rfam database...	0.23	0.33	0.17	17	22339	97	47	37	13	34
3IZ4_A	tmRNA links to Rfam database...	0.52	0.57	0.48	54	25423	63	27	32	4	41
3IZF_C	5S_rRNA links to Rfam database...	0.83	0.86	0.81	30	2603	11	0	7	4	5
3J0L_7	-	-0.02	0.00	0.00	0	504	15	1	14	0	10
3J0L_1	-	0.83	0.77	0.91	10	473	5	0	1	4	3
3J0L_h	-	0.87	0.81	0.93	26	2112	5	1	1	3	6
3J2C_O	-	0.70	0.68	0.72	28	3948	18	3	8	7	13
3NDB_M	-	1.00	1.00	1.00	44	3670	4	0	0	4	0
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NMU_E	-	-0.02	0.00	0.00	0	208	10	5	3	2	3
3NPB_A	SAM links to Rfam database...	0.82	0.73	0.93	27	2249	6	0	2	4	10
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3O58_2	5S_rRNA links to Rfam database...	0.80	0.81	0.81	25	2723	14	0	6	8	6
3OVS_D	-	0.82	0.83	0.83	10	204	2	0	2	0	2
3P22_G	-	0.91	0.91	0.91	10	301	1	0	1	0	1
3R4F_A	-	1.00	1.00	1.00	22	884	1	0	0	1	0
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SIU_F	-	1.00	1.00	1.00	8	137	0	0	0	0	0
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3VJR_D	-	1.00	1.00	1.00	12	239	1	0	0	1	0
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.55	0.56	18	1957	15	4	10	1	15
3ZEX_H	-	0.25	0.37	0.18	7	3586	33	20	12	1	12
3ZEX_E	-	-0.01	0.00	0.00	0	8251	55	17	36	2	34
3ZEX_D	5S_rRNA links to Rfam database...	0.82	0.77	0.87	27	2765	8	0	4	4	8
3ZEX_B	-	0.34	0.38	0.31	132	420926	337	77	217	43	214
3ZEX_F	-	-0.01	0.00	0.00	0	908	12	2	4	6	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4ATO_G	-	0.38	0.43	0.38	3	212	6	5	0	1	4
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4
4FNJ_A	-	0.86	0.83	0.91	10	239	1	0	1	0	2
4HXH_A	-	1.00	1.00	1.00	6	89	1	0	0	1	0

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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 Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

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

Performance of Afold - scored lower in this pairwise comparison

1. Total counts & total scores for Afold

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