CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	McQFold		Cylofold
MCC	0.752	>	0.698
Average MCC ± 95% Confidence Intervals	0.757 ± 0.069	>	0.730 ± 0.064
Sensitivity	0.738	>	0.683
Positive Predictive Value	0.774	>	0.723
Total TP	1024	>	948
Total TN	85094	<	85105
Total FP	407	<	465
Total FP CONTRA	86	<	101
Total FP INCONS	213	<	263
Total FP COMP	108	>	101
Total FN	364	<	440
P-value	3.56938820447e-08

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Performance plots

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

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Performance of McQFold - scored higher in this pairwise comparison

1. Total counts & total scores for McQFold

Total Base Pair Counts
Total TP	1024
Total TN	85094
Total FP	407
Total FP CONTRA	86
Total FP INCONS	213
Total FP COMP	108
Total FN	364

Total Scores
MCC	0.752
Average MCC ± 95% Confidence Intervals	0.757 ± 0.069
Sensitivity	0.738
Positive Predictive Value	0.774
Nr of predictions	74

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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	-	0.75	0.83	0.68	19	1996	15	7	2	6	4
2KX8_A	7SK links to Rfam database...	0.93	0.94	0.94	15	355	1	0	1	0	1
2KXM_A	-	0.78	0.63	1.00	5	144	0	0	0	0	3
2KZL_A	-	1.00	1.00	1.00	13	507	2	0	0	2	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	0	0	0	0	0
2L1F_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	0	0	0	0	0
2L2K_A	-	1.00	1.00	1.00	17	332	1	0	0	1	0
2L3C_B	-	1.00	1.00	1.00	14	225	1	0	0	1	0
2L3E_A	-	1.00	1.00	1.00	12	228	2	0	0	2	0
2L3J_B	mir-2985-2 links to Rfam database...	0.95	0.90	1.00	27	958	0	0	0	0	3
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
2LA5_A	-	0.77	0.71	0.83	5	269	1	0	1	0	2
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	1	4	0	7
2LDL_A	-	0.81	0.67	1.00	6	134	0	0	0	0	3
2LDT_A	-	0.79	0.64	1.00	7	155	0	0	0	0	4
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.55	0.55	0.55	16	2411	15	5	8	2	13
2LWK_A	-	0.95	0.91	1.00	10	197	2	0	0	2	1
2RRC_A	-	0.83	0.71	1.00	5	70	0	0	0	0	2
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.33	0.36	0.31	4	1822	27	2	7	18	7
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.27	0.26	0.30	9	2015	22	0	21	1	26
2Y9C_V	-	0.72	0.72	0.72	13	888	8	0	5	3	5
2YIE_X	-	0.53	0.57	0.50	4	536	6	1	3	2	3
2YIE_Z	-	0.53	0.63	0.45	5	591	6	4	2	0	3
3ADB_C	-	0.98	0.97	1.00	32	1787	1	0	0	1	1
3AKZ_H	tRNA links to Rfam database...	0.78	0.80	0.76	16	1106	7	2	3	2	4
3AM1_B	-	1.00	1.00	1.00	29	1437	1	0	0	1	0
3AMU_B	tRNA links to Rfam database...	0.86	0.79	0.94	15	1141	4	0	1	3	4
3IZF_C	5S_rRNA links to Rfam database...	0.85	0.83	0.88	29	2607	7	0	4	3	6
3J0L_h	-	0.75	0.66	0.88	21	2116	3	0	3	0	11
3J0L_7	-	-0.02	0.00	0.00	0	509	10	2	8	0	10
3J0L_2	-	0.29	0.31	0.30	8	2223	21	1	18	2	18
3J0L_a	-	0.21	0.18	0.29	2	404	6	3	2	1	9
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_1	-	0.73	0.62	0.89	8	475	4	0	1	3	5
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2C_O	-	0.62	0.61	0.64	25	3948	17	3	11	3	16
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.68	0.74	23	2989	11	0	8	3	11
3NDB_M	-	0.97	0.95	0.98	42	3671	5	0	1	4	2
3NKB_B	-	0.42	0.42	0.44	8	717	10	2	8	0	11
3NMU_E	-	0.57	0.33	1.00	1	215	3	0	0	3	2
3O58_3	5_8S_rRNA links to Rfam database...	0.30	0.36	0.25	8	4732	27	15	9	3	14
3O58_2	5S_rRNA links to Rfam database...	0.93	0.87	1.00	27	2727	2	0	0	2	4
3OVB_D	-	1.00	1.00	1.00	11	215	1	0	0	1	0
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
3PDR_A	ykoK links to Rfam database...	0.83	0.80	0.87	40	4794	9	2	4	3	10
3R4F_A	-	1.00	1.00	1.00	22	884	2	0	0	2	0
3R9X_C	-	1.00	1.00	1.00	8	221	2	0	0	2	0
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.82	0.83	0.83	24	1504	5	1	4	0	5
3SIU_F	-	0.86	0.75	1.00	6	139	0	0	0	0	2
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3TRZ_Z	-	1.00	1.00	1.00	5	87	2	0	0	2	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.95	0.91	1.00	20	1256	2	0	0	2	2
3UZL_B	tRNA links to Rfam database...	0.62	0.75	0.52	12	1270	17	8	3	6	4
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.49	0.45	0.54	15	1961	14	1	12	1	18
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.66	0.88	23	2770	6	1	2	3	12
3ZEX_E	-	0.00	0.00	0.00	0	8256	53	17	31	5	34
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ATO_G	-	-0.03	0.00	0.00	0	215	5	0	5	0	7
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FNJ_A	-	-0.04	0.00	0.00	0	243	7	0	7	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	0.93	0.88	1.00	21	1181	0	0	0	0	3
4FRN_A	AdoCbl-variant links to Rfam database...	0.82	0.71	0.95	20	1827	1	1	0	0	8
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

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Performance of Cylofold - scored lower in this pairwise comparison

1. Total counts & total scores for Cylofold

Total Base Pair Counts
Total TP	948
Total TN	85105
Total FP	465
Total FP CONTRA	101
Total FP INCONS	263
Total FP COMP	101
Total FN	440

Total Scores
MCC	0.698
Average MCC ± 95% Confidence Intervals	0.730 ± 0.064
Sensitivity	0.683
Positive Predictive Value	0.723
Nr of predictions	74

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.85	0.87	0.83	20	2000	12	4	0	8	3
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2KXM_A	-	0.78	0.63	1.00	5	144	0	0	0	0	3
2KZL_A	-	0.83	0.69	1.00	9	511	1	0	0	1	4
2L1F_B	Gammaretro_CES links to Rfam database...	0.93	0.88	1.00	21	770	0	0	0	0	3
2L1F_A	Gammaretro_CES links to Rfam database...	0.93	0.87	1.00	20	743	0	0	0	0	3
2L2K_A	-	0.87	0.76	1.00	13	336	0	0	0	0	4
2L3C_B	-	0.84	0.71	1.00	10	229	0	0	0	0	4
2L3E_A	-	1.00	1.00	1.00	12	228	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	0.95	0.90	1.00	27	958	0	0	0	0	3
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
2LA5_A	-	0.77	0.71	0.83	5	269	1	0	1	0	2
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	1	4	0	7
2LDL_A	-	0.81	0.67	1.00	6	134	0	0	0	0	3
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.56	0.55	0.57	16	2412	13	4	8	1	13
2LWK_A	-	0.95	0.91	1.00	10	197	1	0	0	1	1
2RRC_A	-	0.83	0.71	1.00	5	70	0	0	0	0	2
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.41	0.55	0.32	6	1816	25	9	4	12	5
2XQD_Y	tRNA links to Rfam database...	0.89	0.95	0.83	20	1105	5	4	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.10	0.11	0.11	4	2009	32	2	30	0	31
2Y9C_V	-	0.72	0.72	0.72	13	888	8	0	5	3	5
2YIE_X	-	0.43	0.57	0.33	4	532	10	2	6	2	3
2YIE_Z	-	-0.02	0.00	0.00	0	591	11	5	6	0	8
3ADB_C	-	0.84	0.82	0.87	27	1788	4	0	4	0	6
3AKZ_H	tRNA links to Rfam database...	0.77	0.75	0.79	15	1108	7	0	4	3	5
3AM1_B	-	0.83	0.76	0.92	22	1442	2	0	2	0	7
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3IZF_C	5S_rRNA links to Rfam database...	0.85	0.83	0.88	29	2607	7	0	4	3	6
3J0L_h	-	0.55	0.50	0.62	16	2114	10	2	8	0	16
3J0L_7	-	0.41	0.50	0.36	5	505	10	3	6	1	5
3J0L_2	-	0.49	0.46	0.52	12	2227	18	0	11	7	14
3J0L_a	-	0.17	0.18	0.20	2	401	9	3	5	1	9
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_1	-	0.73	0.62	0.89	8	475	3	0	1	2	5
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3J20_1	tRNA links to Rfam database...	0.71	0.75	0.68	15	1090	8	2	5	1	5
3J2C_O	-	0.51	0.49	0.54	20	3950	19	1	16	2	21
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.68	0.74	23	2989	11	0	8	3	11
3NDB_M	-	0.68	0.64	0.74	28	3676	14	2	8	4	16
3NKB_B	-	0.46	0.42	0.53	8	720	7	0	7	0	11
3NMU_E	-	0.28	0.33	0.25	1	212	6	1	2	3	2
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.50	0.35	11	4733	30	9	11	10	11
3O58_2	5S_rRNA links to Rfam database...	0.90	0.84	0.96	26	2727	3	0	1	2	5
3OVB_D	-	1.00	1.00	1.00	11	215	1	0	0	1	0
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
3PDR_A	ykoK links to Rfam database...	0.86	0.78	0.95	39	4799	4	1	1	2	11
3R4F_A	-	1.00	1.00	1.00	22	884	1	0	0	1	0
3R9X_C	-	1.00	1.00	1.00	8	221	2	0	0	2	0
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.71	0.69	0.74	20	1506	7	2	5	0	9
3SIU_F	-	0.86	0.75	1.00	6	139	0	0	0	0	2
3SN2_B	IRE_II links to Rfam database...	0.63	0.42	1.00	5	149	0	0	0	0	7
3TRZ_Z	-	1.00	1.00	1.00	5	87	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3UZL_B	tRNA links to Rfam database...	0.45	0.50	0.42	8	1274	18	4	7	7	8
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.48	0.45	0.52	15	1960	15	1	13	1	18
3ZEX_D	5S_rRNA links to Rfam database...	0.69	0.69	0.71	24	2762	11	5	5	1	11
3ZEX_E	-	0.00	0.00	0.00	0	8258	51	15	31	5	34
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ATO_G	-	0.88	1.00	0.78	7	211	2	2	0	0	0
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FNJ_A	-	0.81	0.67	1.00	8	242	0	0	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.93	0.88	1.00	21	1181	0	0	0	0	3
4FRN_A	AdoCbl-variant links to Rfam database...	0.23	0.18	0.31	5	1832	11	7	4	0	23
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	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 McQFold - scored higher in this pairwise comparison

1. Total counts & total scores for McQFold

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

Performance of Cylofold - scored lower in this pairwise comparison

1. Total counts & total scores for Cylofold

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