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		MCFold
MCC	0.763	>	0.675
Average MCC ± 95% Confidence Intervals	0.778 ± 0.057	>	0.699 ± 0.067
Sensitivity	0.750	>	0.715
Positive Predictive Value	0.785	>	0.650
Total TP	1272	>	1213
Total TN	89305	>	89059
Total FP	496	<	900
Total FP CONTRA	112	<	175
Total FP INCONS	236	<	478
Total FP COMP	148	<	247
Total FN	425	<	484
P-value	3.56938820447e-08

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Performance plots

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

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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	1272
Total TN	89305
Total FP	496
Total FP CONTRA	112
Total FP INCONS	236
Total FP COMP	148
Total FN	425

Total Scores
MCC	0.763
Average MCC ± 95% Confidence Intervals	0.778 ± 0.057
Sensitivity	0.750
Positive Predictive Value	0.785
Nr of predictions	108

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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
2K5Z_A	-	0.59	0.36	1.00	4	182	0	0	0	0	7
2K63_A	-	1.00	1.00	1.00	9	159	0	0	0	0	0
2K66_A	-	1.00	1.00	1.00	9	80	0	0	0	0	0
2KD8_A	-	1.00	1.00	1.00	9	99	1	0	0	1	0
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	0.91	0.83	1.00	15	452	1	0	0	1	3
2KEZ_A	-	1.00	1.00	1.00	8	94	0	0	0	0	0
2KFC_A	-	0.79	0.63	1.00	5	231	0	0	0	0	3
2KGP_A	-	0.81	0.67	1.00	6	115	1	0	0	1	3
2KMJ_A	-	1.00	1.00	1.00	11	157	1	0	0	1	0
2KPV_A	-	0.96	0.92	1.00	12	201	0	0	0	0	1
2KU0_A	-	0.86	0.75	1.00	9	283	0	0	0	0	3
2KUR_A	K10_TLS links to Rfam database...	0.91	0.84	1.00	16	451	0	0	0	0	3
2KUU_A	K10_TLS links to Rfam database...	0.91	0.83	1.00	15	432	1	0	0	1	3
2KUV_A	K10_TLS links to Rfam database...	0.91	0.84	1.00	16	423	0	0	0	0	3
2KUW_A	K10_TLS links to Rfam database...	0.94	0.89	1.00	16	454	0	0	0	0	2
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_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	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
2LBS_A	-	1.00	1.00	1.00	14	193	1	0	0	1	0
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
2LHP_A	-	1.00	1.00	1.00	15	246	1	0	0	1	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	-	0.55	0.55	0.55	16	2411	15	5	8	2	13
2LQZ_A	-	1.00	1.00	1.00	8	124	3	0	0	3	0
2LWK_A	-	0.95	0.91	1.00	10	197	2	0	0	2	1
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2RPT_A	-	1.00	1.00	1.00	7	65	0	0	0	0	0
2RRC_A	-	0.83	0.71	1.00	5	70	0	0	0	0	2
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2WW9_E	-	-0.03	0.00	0.00	0	168	5	0	4	1	5
2WW9_D	-	0.44	0.40	0.50	4	733	9	4	0	5	6
2WW9_F	-	0.86	0.75	1.00	6	106	1	0	0	1	2
2WWQ_V	tRNA links to Rfam database...	0.00	0.00	0.00	0	1204	0	0	0	0	19
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
2Y8W_B	-	1.00	1.00	1.00	6	82	2	0	0	2	0
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
2ZY6_A	-	0.66	0.78	0.58	7	264	5	3	2	0	2
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	2	2	0	0	1
3A2K_C	tRNA links to Rfam database...	0.98	0.95	1.00	21	1087	0	0	0	0	1
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
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
3DW4_A	-	-0.03	0.00	0.00	0	137	3	0	3	0	6
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.56	0.57	0.57	16	1421	13	4	8	1	12
3HAY_E	-	1.00	1.00	1.00	14	910	4	0	0	4	0
3HJW_D	-	0.94	0.94	0.94	15	593	3	0	1	2	1
3IAB_R	-	1.00	1.00	1.00	12	373	0	0	0	0	0
3ID5_D	-	0.66	0.60	0.75	3	225	6	0	1	5	2
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.21	0.21	0.24	6	1447	19	2	17	0	22
3IZF_C	5S_rRNA links to Rfam database...	0.85	0.83	0.88	29	2607	7	0	4	3	6
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.21	0.18	0.29	2	404	6	3	2	1	9
3J0L_1	-	0.73	0.62	0.89	8	475	4	0	1	3	5
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_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_2	-	0.29	0.31	0.30	8	2223	21	1	18	2	18
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1091	20	4	16	0	20
3JYX_4	5_8S_rRNA links to Rfam database...	0.35	0.58	0.22	7	4724	33	17	8	8	5
3JYX_3	5S_rRNA links to Rfam database...	0.28	0.40	0.20	6	2348	24	17	7	0	9
3KTW_C	-	0.52	0.52	0.54	13	1756	17	2	9	6	12
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
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_2	5S_rRNA links to Rfam database...	0.93	0.87	1.00	27	2727	2	0	0	2	4
3O58_3	5_8S_rRNA links to Rfam database...	0.30	0.36	0.25	8	4732	27	15	9	3	14
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
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	-	0.95	0.91	1.00	20	1256	2	0	0	2	2
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	33	11	16	6	15
4A1C_3	5S_rRNA links to Rfam database...	0.28	0.30	0.28	11	2724	30	4	24	2	26
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	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

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Performance of MCFold - scored lower in this pairwise comparison

1. Total counts & total scores for MCFold

Total Base Pair Counts
Total TP	1213
Total TN	89059
Total FP	900
Total FP CONTRA	175
Total FP INCONS	478
Total FP COMP	247
Total FN	484

Total Scores
MCC	0.675
Average MCC ± 95% Confidence Intervals	0.699 ± 0.067
Sensitivity	0.715
Positive Predictive Value	0.650
Nr of predictions	108

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2K5Z_A	-	1.00	1.00	1.00	11	175	0	0	0	0	0
2K63_A	-	1.00	1.00	1.00	9	159	4	0	0	4	0
2K66_A	-	1.00	1.00	1.00	9	80	0	0	0	0	0
2KD8_A	-	1.00	1.00	1.00	9	99	1	0	0	1	0
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	1	0	0	1	0
2KE6_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	449	1	0	0	1	0
2KEZ_A	-	1.00	1.00	1.00	8	94	0	0	0	0	0
2KFC_A	-	0.54	0.63	0.50	5	226	5	2	3	0	3
2KGP_A	-	1.00	1.00	1.00	9	112	1	0	0	1	0
2KMJ_A	-	1.00	1.00	1.00	11	157	1	0	0	1	0
2KPV_A	-	1.00	1.00	1.00	13	200	0	0	0	0	0
2KU0_A	-	1.00	1.00	1.00	12	280	1	0	0	1	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	1	0	0	1	0
2KZL_A	-	1.00	1.00	1.00	13	507	5	0	0	5	0
2L1F_A	Gammaretro_CES links to Rfam database...	0.79	0.78	0.82	18	741	4	0	4	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.80	0.79	0.83	19	768	4	0	4	0	5
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...	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	-	-0.03	0.00	0.00	0	265	10	0	10	0	7
2LBS_A	-	1.00	1.00	1.00	14	193	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.44	0.44	0.47	8	511	10	0	9	1	10
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LDT_A	-	0.95	0.91	1.00	10	152	0	0	0	0	1
2LHP_A	-	1.00	1.00	1.00	15	246	1	0	0	1	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	11	0	0	11	0
2LQZ_A	-	1.00	1.00	1.00	8	124	3	0	0	3	0
2LWK_A	-	1.00	1.00	1.00	11	196	2	0	0	2	0
2RP0_A	-	0.70	0.71	0.71	5	109	2	1	1	0	2
2RPT_A	-	1.00	1.00	1.00	7	65	0	0	0	0	0
2RRC_A	-	1.00	1.00	1.00	7	68	1	0	0	1	0
2WRQ_Y	tRNA links to Rfam database...	0.38	0.56	0.26	5	1133	21	8	6	7	4
2WW9_E	-	-0.03	0.00	0.00	0	165	8	1	6	1	5
2WW9_D	-	-0.02	0.00	0.00	0	723	21	6	12	3	10
2WW9_F	-	0.68	0.75	0.67	6	103	4	1	2	1	2
2WWQ_V	tRNA links to Rfam database...	0.19	0.21	0.19	4	1183	20	3	14	3	15
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.20	0.27	0.16	3	1816	30	4	12	14	8
2XQD_Y	tRNA links to Rfam database...	0.39	0.43	0.38	9	1105	18	2	13	3	12
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.23	0.26	0.24	9	2007	30	1	28	1	26
2Y8W_B	-	1.00	1.00	1.00	6	82	2	0	0	2	0
2Y9C_V	-	0.65	0.72	0.59	13	884	12	1	8	3	5
2YIE_X	-	-0.01	0.00	0.00	0	535	15	1	8	6	7
2YIE_Z	-	0.53	0.63	0.45	5	591	8	2	4	2	3
2ZY6_A	-	0.77	0.78	0.78	7	267	6	1	1	4	2
2ZZN_D	tRNA links to Rfam database...	0.69	0.73	0.67	16	960	11	1	7	3	6
3A2K_C	tRNA links to Rfam database...	0.49	0.55	0.46	12	1082	14	3	11	0	10
3A3A_A	tRNA-Sec links to Rfam database...	0.98	0.97	1.00	29	1471	0	0	0	0	1
3AKZ_H	tRNA links to Rfam database...	0.46	0.50	0.43	10	1104	16	5	8	3	10
3AM1_B	-	1.00	1.00	1.00	29	1437	1	0	0	1	0
3AMU_B	tRNA links to Rfam database...	0.50	0.58	0.44	11	1132	15	4	10	1	8
3DW4_A	-	1.00	1.00	1.00	6	134	3	0	0	3	0
3GCA_A	-	-0.05	0.00	0.00	0	150	8	4	4	0	7
3GX2_A	SAM links to Rfam database...	0.58	0.61	0.57	17	1419	15	1	12	2	11
3HAY_E	-	1.00	1.00	1.00	14	910	10	0	0	10	0
3HJW_D	-	1.00	1.00	1.00	16	593	5	0	0	5	0
3IAB_R	-	1.00	1.00	1.00	12	373	4	0	0	4	0
3ID5_D	-	0.54	0.60	0.50	3	223	7	1	2	4	2
3IVN_B	Purine links to Rfam database...	0.45	0.48	0.46	11	879	14	5	8	1	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.19	0.21	0.20	6	1442	24	5	19	0	22
3IZF_C	5S_rRNA links to Rfam database...	0.92	0.94	0.89	33	2603	10	0	4	6	2
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.14	0.18	0.15	2	398	13	1	10	2	9
3J0L_1	-	0.88	0.85	0.92	11	472	5	0	1	4	2
3J0L_h	-	0.98	0.97	1.00	31	2109	2	0	0	2	1
3J0L_7	-	-0.02	0.00	0.00	0	504	15	6	9	0	10
3J0L_g	-	-0.02	0.00	0.00	0	170	7	4	2	1	2
3J0L_2	-	0.25	0.27	0.25	7	2222	29	4	17	8	19
3J16_L	tRNA links to Rfam database...	0.54	0.57	0.52	12	1136	12	4	7	1	9
3JYV_7	tRNA links to Rfam database...	0.25	0.30	0.24	6	1086	20	8	11	1	14
3JYX_4	5_8S_rRNA links to Rfam database...	0.36	0.58	0.23	7	4725	37	19	5	13	5
3JYX_3	5S_rRNA links to Rfam database...	0.46	0.67	0.32	10	2347	28	15	6	7	5
3KTW_C	-	0.55	0.60	0.52	15	1751	20	4	10	6	10
3LA5_A	Purine links to Rfam database...	0.44	0.44	0.48	11	931	12	2	10	0	14
3NDB_M	-	0.29	0.30	0.30	13	3671	35	1	29	5	31
3NKB_B	-	0.68	0.74	0.64	14	713	8	2	6	0	5
3NMU_E	-	0.51	0.67	0.40	2	211	8	1	2	5	1
3O58_2	5S_rRNA links to Rfam database...	0.25	0.29	0.23	9	2715	31	6	24	1	22
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.36	0.22	8	4727	39	14	15	10	14
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	1	0	0	1	0
3PDR_A	ykoK links to Rfam database...	0.78	0.80	0.77	40	4788	14	5	7	2	10
3R4F_A	-	0.95	0.95	0.95	21	884	4	0	1	3	1
3R9X_C	-	0.87	0.88	0.88	7	221	5	0	1	4	1
3RKF_A	Purine links to Rfam database...	0.89	0.88	0.91	21	843	3	0	2	1	3
3SD1_A	THF links to Rfam database...	0.43	0.45	0.43	13	1503	17	1	16	0	16
3SIU_F	-	0.53	0.63	0.50	5	135	5	2	3	0	3
3SN2_B	IRE_II links to Rfam database...	0.58	0.58	0.64	7	143	4	0	4	0	5
3TRZ_Z	-	-0.05	0.00	0.00	0	88	4	0	4	0	5
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	-0.05	0.00	0.00	0	102	7	0	6	1	5
3U4M_B	-	0.74	0.77	0.71	17	1252	10	1	6	3	5
3VJR_D	-	1.00	1.00	1.00	12	239	1	0	0	1	0
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4480	45	12	19	14	15
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.86	0.86	32	2726	9	0	5	4	5
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4ENB_A	crcB links to Rfam database...	0.78	0.73	0.85	11	459	4	0	2	2	4
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	11	0	8	3	10

^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 McQFold - scored higher in this pairwise comparison

1. Total counts & total scores for McQFold

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

Performance of MCFold - scored lower in this pairwise comparison

1. Total counts & total scores for MCFold

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