CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	PknotsRG		Cylofold
MCC	0.743	>	0.701
Average MCC ± 95% Confidence Intervals	0.781 ± 0.063	>	0.734 ± 0.064
Sensitivity	0.757	>	0.686
Positive Predictive Value	0.738	>	0.725
Total TP	1061	>	962
Total TN	85168	<	85280
Total FP	516	>	465
Total FP CONTRA	93	<	101
Total FP INCONS	284	>	263
Total FP COMP	139	>	101
Total FN	341	<	440
P-value	3.56938820447e-08

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Performance plots

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

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Performance of PknotsRG - scored higher in this pairwise comparison

1. Total counts & total scores for PknotsRG

Total Base Pair Counts
Total TP	1061
Total TN	85168
Total FP	516
Total FP CONTRA	93
Total FP INCONS	284
Total FP COMP	139
Total FN	341

Total Scores
MCC	0.743
Average MCC ± 95% Confidence Intervals	0.781 ± 0.063
Sensitivity	0.757
Positive Predictive Value	0.738
Nr of predictions	75

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2. Individual counts for PknotsRG [ 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	-	0.93	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...	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	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
2LA5_A	-	0.77	0.71	0.83	5	269	3	0	1	2	2
2LC8_A	GP_knot1 links to Rfam database...	0.66	0.61	0.73	11	513	4	2	2	0	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
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.81	0.86	0.76	25	2407	10	6	2	2	4
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...	0.64	0.73	0.57	8	1821	24	0	6	18	3
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...	0.35	0.34	0.38	12	2013	21	1	19	1	23
2Y9C_V	-	0.79	0.83	0.75	15	886	8	0	5	3	3
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
2YIE_X	-	0.43	0.57	0.33	4	532	10	2	6	2	3
3ADB_C	-	0.35	0.36	0.36	12	1786	21	1	20	0	21
3AKZ_H	tRNA links to Rfam database...	0.46	0.50	0.43	10	1104	15	6	7	2	10
3AM1_B	-	0.74	0.76	0.73	22	1436	8	3	5	0	7
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3IZF_C	5S_rRNA links to Rfam database...	0.75	0.77	0.73	27	2603	15	0	10	5	8
3J0L_7	-	0.38	0.50	0.31	5	503	12	3	8	1	5
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
3J0L_2	-	0.29	0.31	0.29	8	2222	27	2	18	7	18
3J0L_1	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_h	-	0.87	0.81	0.93	26	2112	4	1	1	2	6
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J2C_O	-	0.71	0.71	0.73	29	3947	17	2	9	6	12
3J2L_3	5S_rRNA links to Rfam database...	0.80	0.82	0.78	28	2984	12	1	7	4	6
3NDB_M	-	0.93	0.93	0.93	41	3670	9	0	3	6	3
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NMU_E	-	1.00	1.00	1.00	3	213	5	0	0	5	0
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	35	6	15	14	11
3O58_2	5S_rRNA links to Rfam database...	0.72	0.74	0.70	23	2721	19	0	10	9	8
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...	0.90	0.90	0.90	45	4790	7	2	3	2	5
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...	0.73	0.72	0.75	21	1505	7	4	3	0	8
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
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...	0.49	0.50	0.50	8	1277	15	0	8	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...	0.64	0.64	0.66	21	1957	12	4	7	1	12
3ZEX_D	5S_rRNA links to Rfam database...	0.88	0.83	0.94	29	2765	6	0	2	4	6
3ZEX_E	-	0.00	0.00	0.00	0	8254	55	17	33	5	34
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
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	-	0.91	0.83	1.00	10	240	0	0	0	0	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.59	0.57	0.62	16	1822	10	2	8	0	12
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	962
Total TN	85280
Total FP	465
Total FP CONTRA	101
Total FP INCONS	263
Total FP COMP	101
Total FN	440

Total Scores
MCC	0.701
Average MCC ± 95% Confidence Intervals	0.734 ± 0.064
Sensitivity	0.686
Positive Predictive Value	0.725
Nr of predictions	75

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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
2LI4_A	-	1.00	1.00	1.00	14	175	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_Z	-	-0.02	0.00	0.00	0	591	11	5	6	0	8
2YIE_X	-	0.43	0.57	0.33	4	532	10	2	6	2	3
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_7	-	0.41	0.50	0.36	5	505	10	3	6	1	5
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_a	-	0.17	0.18	0.20	2	401	9	3	5	1	9
3J0L_2	-	0.49	0.46	0.52	12	2227	18	0	11	7	14
3J0L_1	-	0.73	0.62	0.89	8	475	3	0	1	2	5
3J0L_h	-	0.55	0.50	0.62	16	2114	10	2	8	0	16
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
3J20_1	tRNA links to Rfam database...	0.71	0.75	0.68	15	1090	8	2	5	1	5
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	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 PknotsRG - scored higher in this pairwise comparison

1. Total counts & total scores for PknotsRG

2. Individual counts for PknotsRG [ 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 ]