CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Sfold		Fold
MCC	0.671	>	0.636
Average MCC ± 95% Confidence Intervals	0.778 ± 0.055	>	0.755 ± 0.065
Sensitivity	0.674	>	0.668
Positive Predictive Value	0.670	>	0.608
Total TP	1871	>	1853
Total TN	1045955	>	1045701
Total FP	1261	<	1541
Total FP CONTRA	256	<	343
Total FP INCONS	666	<	851
Total FP COMP	339	<	347
Total FN	903	<	921
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP	1871
Total TN	1045955
Total FP	1261
Total FP CONTRA	256
Total FP INCONS	666
Total FP COMP	339
Total FN	903

Total Scores
MCC	0.671
Average MCC ± 95% Confidence Intervals	0.778 ± 0.055
Sensitivity	0.674
Positive Predictive Value	0.670
Nr of predictions	101

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2. Individual counts for Sfold [ 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
2KRL_A	-	0.91	0.87	0.95	20	2003	9	1	0	8	3
2KU0_A	-	0.96	0.92	1.00	11	281	0	0	0	0	1
2KUR_A	K10_TLS links to Rfam database...	0.95	0.95	0.95	18	448	1	0	1	0	1
2KUU_A	K10_TLS links to Rfam database...	0.94	0.94	0.94	17	429	2	0	1	1	1
2KUV_A	K10_TLS links to Rfam database...	0.94	0.95	0.95	18	420	1	0	1	0	1
2KUW_A	K10_TLS links to Rfam database...	0.94	0.94	0.94	17	452	2	0	1	1	1
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_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	0	0	0	0	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	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
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.39	0.58	7	516	5	0	5	0	11
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	-	0.95	0.90	1.00	26	2414	6	0	0	6	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
2RRC_A	-	1.00	1.00	1.00	7	68	0	0	0	0	0
2WWQ_V	tRNA links to Rfam database...	1.00	1.00	1.00	19	1185	2	0	0	2	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	25	0	6	19	3
2XQD_Y	tRNA links to Rfam database...	0.85	0.81	0.89	17	1110	3	0	2	1	4
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.37	0.34	0.41	12	2016	18	1	16	1	23
2Y8W_B	-	1.00	1.00	1.00	6	82	1	0	0	1	0
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	-	0.75	0.57	1.00	4	540	0	0	0	0	3
3ADB_C	-	0.67	0.64	0.72	21	1790	9	0	8	1	12
3AKZ_H	tRNA links to Rfam database...	0.49	0.50	0.50	10	1107	12	3	7	2	10
3AM1_B	-	0.75	0.76	0.76	22	1437	7	3	4	0	7
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3IYQ_A	tmRNA links to Rfam database...	0.25	0.33	0.19	17	22350	86	39	34	13	34
3IZ4_A	tmRNA links to Rfam database...	0.59	0.56	0.63	53	25452	34	14	17	3	42
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	8	0	5	3	3
3J0L_7	-	-0.01	0.00	0.00	0	516	3	1	2	0	10
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.55	0.64	0.50	7	397	8	5	2	1	4
3J0L_2	-	0.44	0.42	0.48	11	2227	19	0	12	7	15
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	4	1	1	2	6
3J0L_g	-	-0.01	0.00	0.00	0	173	5	1	2	2	2
3J16_L	tRNA links to Rfam database...	0.34	0.33	0.37	7	1140	12	0	12	0	14
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	7	0	5	2	5
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.57	0.58	0.56	240	421940	241	31	157	53	172
3J2C_M	-	0.85	0.85	0.85	82	39828	51	6	9	36	14
3J2C_O	-	0.76	0.66	0.87	27	3956	9	2	2	5	14
3J2L_3	5S_rRNA links to Rfam database...	0.80	0.82	0.78	28	2984	12	1	7	4	6
3NDB_M	-	0.96	0.93	1.00	41	3673	4	0	0	4	3
3NKB_B	-	0.75	0.74	0.78	14	717	4	0	4	0	5
3NMU_E	-	1.00	1.00	1.00	3	213	4	0	0	4	0
3NPB_A	SAM links to Rfam database...	0.85	0.78	0.94	29	2247	7	0	2	5	8
3O58_2	5S_rRNA links to Rfam database...	0.87	0.90	0.85	28	2721	11	0	5	6	3
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.50	0.52	11	4743	18	2	8	8	11
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...	0.82	0.80	0.85	40	4793	9	2	5	2	10
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...	0.78	0.72	0.84	21	1508	4	2	2	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	2	0	0	2	0
3TS0_U	-	1.00	1.00	1.00	6	112	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...	0.60	0.50	0.73	8	1282	7	3	0	4	8
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.63	0.64	0.64	21	1956	13	4	8	1	12
3ZEX_F	-	0.00	0.00	0.00	0	914	7	0	0	7	4
3ZEX_G	-	0.99	0.98	1.00	44	6463	15	0	0	15	1
3ZEX_E	-	-0.01	0.00	0.00	0	8250	56	20	34	2	34
3ZEX_D	5S_rRNA links to Rfam database...	0.85	0.80	0.90	28	2765	8	0	3	5	7
3ZEX_B	-	0.37	0.39	0.35	136	420960	296	65	191	40	210
3ZEX_H	-	0.26	0.37	0.19	7	3589	29	18	11	0	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.41	0.34	0.50	10	5354	27	2	8	17	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	34	8	14	12	15
4A1C_3	5S_rRNA links to Rfam database...	0.83	0.81	0.86	30	2728	7	0	5	2	7
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	-	0.37	0.14	1.00	1	219	0	0	0	0	6
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.57	0.33	1.00	5	491	0	0	0	0	10
4FNJ_A	-	0.91	0.83	1.00	10	240	0	0	0	0	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.67	0.58	0.78	14	1184	4	3	1	0	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.71	0.57	0.89	16	1830	2	2	0	0	12
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

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Performance of Fold - scored lower in this pairwise comparison

1. Total counts & total scores for Fold

Total Base Pair Counts
Total TP	1853
Total TN	1045701
Total FP	1541
Total FP CONTRA	343
Total FP INCONS	851
Total FP COMP	347
Total FN	921

Total Scores
MCC	0.636
Average MCC ± 95% Confidence Intervals	0.755 ± 0.065
Sensitivity	0.668
Positive Predictive Value	0.608
Nr of predictions	101

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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
2KRL_A	-	0.91	0.87	0.95	20	2003	9	1	0	8	3
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_A	Gammaretro_CES links to Rfam database...	0.91	0.91	0.91	21	740	2	0	2	0	2
2L1F_B	Gammaretro_CES links to Rfam database...	0.91	0.92	0.92	22	767	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
2LA5_A	-	0.77	0.71	0.83	5	269	3	0	1	2	2
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
2RRC_A	-	0.83	0.71	1.00	5	70	0	0	0	0	2
2WWQ_V	tRNA links to Rfam database...	0.97	0.95	1.00	18	1186	3	0	0	3	1
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	26	0	6	20	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...	1.00	1.00	1.00	35	2010	1	0	0	1	0
2Y8W_B	-	1.00	1.00	1.00	6	82	1	0	0	1	0
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	-	0.39	0.43	0.38	3	536	8	1	4	3	4
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
3AMU_B	tRNA links to Rfam database...	0.73	0.79	0.68	15	1135	10	0	7	3	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_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.15	0.18	0.17	2	399	11	4	6	1	9
3J0L_2	-	0.30	0.31	0.31	8	2224	25	2	16	7	18
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
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J16_L	tRNA links to Rfam database...	0.76	0.76	0.76	16	1138	5	0	5	0	5
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.55	0.58	0.53	239	421918	270	31	180	59	173
3J2C_M	-	0.23	0.27	0.20	26	39796	116	31	72	13	70
3J2C_O	-	0.71	0.76	0.67	31	3941	21	5	10	6	10
3J2L_3	5S_rRNA links to Rfam database...	0.80	0.82	0.78	28	2984	12	1	7	4	6
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_2	5S_rRNA links to Rfam database...	0.86	0.87	0.84	27	2722	12	0	5	7	4
3O58_3	5_8S_rRNA links to Rfam database...	0.39	0.50	0.31	11	4728	41	9	16	16	11
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...	0.93	0.92	0.94	46	4791	5	1	2	2	4
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...	0.68	0.69	0.69	20	1504	9	4	5	0	9
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
3TRZ_Z	-	1.00	1.00	1.00	5	87	1	0	0	1	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
3UZL_B	tRNA links to Rfam database...	1.00	1.00	1.00	16	1277	8	0	0	8	0
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_F	-	-0.01	0.00	0.00	0	908	11	2	4	5	4
3ZEX_G	-	0.98	0.96	1.00	43	6464	17	0	0	17	2
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_H	-	0.26	0.37	0.19	7	3588	30	19	11	0	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.28	0.34	0.23	10	5330	46	9	25	12	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4482	43	11	18	14	15
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.84	0.89	31	2728	7	0	4	3	6
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	-	0.38	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
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	8	0	7	1	10
4FNJ_A	-	0.91	0.83	1.00	10	240	0	0	0	0	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.22	0.25	0.23	6	1176	20	7	13	0	18
4FRN_A	AdoCbl-variant links to Rfam database...	0.46	0.46	0.46	13	1820	15	7	8	0	15
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

^top

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 Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

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

Performance of Fold - scored lower in this pairwise comparison

1. Total counts & total scores for Fold

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