CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ProbKnot		McQFold
MCC	0.535	>	0.482
Average MCC ± 95% Confidence Intervals	0.658 ± 0.062	>	0.649 ± 0.064
Sensitivity	0.478	>	0.416
Positive Predictive Value	0.599	>	0.559
Total TP	1848	>	1608
Total TN	2714306	<	2714514
Total FP	1364	>	1361
Total FP CONTRA	149	>	133
Total FP INCONS	1089	<	1137
Total FP COMP	126	>	91
Total FN	2015	<	2255
P-value	3.56938820447e-08

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Performance plots

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

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Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	1848
Total TN	2714306
Total FP	1364
Total FP CONTRA	149
Total FP INCONS	1089
Total FP COMP	126
Total FN	2015

Total Scores
MCC	0.535
Average MCC ± 95% Confidence Intervals	0.658 ± 0.062
Sensitivity	0.478
Positive Predictive Value	0.599
Nr of predictions	92

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.69	0.60	0.80	24	5121	11	2	4	5	16
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2KXM_A	-	0.78	0.70	0.88	7	343	1	0	1	0	3
2KZL_A	-	0.83	0.74	0.93	14	1470	1	0	1	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L2K_A	-	0.94	0.89	1.00	17	844	0	0	0	0	2
2L3C_B	-	0.91	0.82	1.00	14	547	0	0	0	0	3
2L3E_A	-	0.96	0.92	1.00	12	583	1	0	0	1	1
2L3J_B	mir-2985-2 links to Rfam database...	0.94	0.88	1.00	30	2455	0	0	0	0	4
2L5Z_A	-	0.86	0.75	1.00	9	316	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LA5_A	-	0.45	0.32	0.67	6	621	3	0	3	0	13
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
2LJJ_A	-	1.00	1.00	1.00	8	343	2	0	0	2	0
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.85	0.77	0.94	30	6073	4	0	2	2	9
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.88	0.85	0.92	11	484	1	0	1	0	2
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	24	0	9	15	10
2XQD_Y	tRNA links to Rfam database...	0.90	0.81	1.00	22	2828	1	0	0	1	5
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.26	0.24	0.29	10	5116	25	1	24	0	32
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
2Y9C_V	-	0.65	0.63	0.68	15	2256	8	1	6	1	9
2YIE_X	-	0.34	0.33	0.36	4	1367	7	2	5	0	8
2YIE_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
3AKZ_H	tRNA links to Rfam database...	0.73	0.75	0.72	21	2672	8	4	4	0	7
3AM1_B	-	0.74	0.71	0.78	25	3208	7	1	6	0	10
3AMU_B	tRNA links to Rfam database...	0.65	0.59	0.73	16	2981	8	0	6	2	11
3IYQ_A	tmRNA links to Rfam database...	0.28	0.31	0.26	29	60616	85	22	59	4	65
3IZ4_A	tmRNA links to Rfam database...	0.52	0.46	0.60	61	70774	46	6	35	5	71
3IZF_C	5S_rRNA links to Rfam database...	0.72	0.61	0.85	33	6864	6	0	6	0	21
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_1	-	0.76	0.63	0.92	12	1212	3	0	1	2	7
3J0L_g	-	-0.01	0.00	0.00	0	458	7	2	5	0	4
3J0L_2	-	0.27	0.27	0.28	9	6184	26	2	21	3	24
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_a	-	0.55	0.50	0.62	8	1115	5	2	3	0	8
3J0L_h	-	0.77	0.65	0.90	28	6074	3	0	3	0	15
3J16_L	tRNA links to Rfam database...	0.35	0.33	0.38	10	2749	16	1	15	0	20
3J20_1	tRNA links to Rfam database...	0.71	0.70	0.73	16	2904	7	0	6	1	7
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.50	0.43	0.57	272	1116290	208	11	192	5	361
3J20_0	tRNA links to Rfam database...	0.45	0.40	0.52	12	2827	12	0	11	1	18
3J2C_M	-	0.37	0.30	0.45	63	106352	79	9	67	3	144
3J2C_O	-	0.60	0.52	0.70	33	10249	15	0	14	1	30
3J2L_3	5S_rRNA links to Rfam database...	0.60	0.49	0.74	26	7840	11	0	9	2	27
3NDB_M	-	0.77	0.69	0.88	42	9132	7	0	6	1	19
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NMU_E	-	-0.01	0.00	0.00	0	552	11	2	7	2	6
3NPB_A	SAM links to Rfam database...	0.72	0.61	0.85	28	6988	8	1	4	3	18
3O58_2	5S_rRNA links to Rfam database...	0.76	0.76	0.76	29	7222	10	3	6	1	9
3O58_3	5_8S_rRNA links to Rfam database...	0.31	0.34	0.29	12	12362	41	4	25	12	23
3OVB_D	-	1.00	1.00	1.00	11	584	2	0	0	2	0
3OVS_D	-	0.92	0.92	0.92	12	548	1	0	1	0	1
3P22_G	-	0.96	0.92	1.00	11	730	1	0	0	1	1
3PDR_A	ykoK links to Rfam database...	0.74	0.64	0.85	46	12826	10	1	7	2	26
3R4F_A	-	0.96	0.92	1.00	23	2122	0	0	0	0	2
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
3RKF_A	Purine links to Rfam database...	0.73	0.59	0.91	20	2189	2	1	1	0	14
3SD1_A	THF links to Rfam database...	0.55	0.48	0.65	20	3885	11	2	9	0	22
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	0	5
3SN2_B	IRE_II links to Rfam database...	1.00	1.00	1.00	12	394	0	0	0	0	0
3TRZ_Z	-	0.91	0.83	1.00	5	205	2	0	0	2	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.45	0.35	0.59	13	3138	9	1	8	0	24
3UZL_B	tRNA links to Rfam database...	0.73	0.62	0.85	23	3543	4	0	4	0	14
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.89	0.80	1.00	32	4721	1	0	0	1	8
3ZEX_E	-	0.00	0.00	0.00	0	21886	61	2	57	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.77	0.67	0.89	33	6984	4	0	4	0	16
3ZEX_F	-	0.00	0.00	0.00	0	2620	11	2	6	3	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.38	0.31	0.47	16	14162	21	2	16	3	36
3ZEX_H	-	0.19	0.18	0.19	7	9009	29	4	25	0	31
3ZEX_B	-	0.29	0.26	0.33	146	1071940	307	34	260	13	412
3ZEX_G	-	0.77	0.66	0.91	49	16417	10	0	5	5	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.12	5	11738	49	7	31	11	28
4A1C_3	5S_rRNA links to Rfam database...	0.73	0.61	0.87	33	7102	6	1	4	1	21
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ATO_G	-	0.32	0.30	0.38	3	520	5	1	4	0	7
4ENB_A	crcB links to Rfam database...	0.73	0.58	0.92	11	1263	1	1	0	0	8
4ENC_A	crcB links to Rfam database...	0.45	0.42	0.50	8	1310	8	1	7	0	11
4FNJ_A	-	0.66	0.50	0.89	8	586	1	0	1	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.37	0.31	0.45	10	3464	12	3	9	0	22
4FRN_A	AdoCbl-variant links to Rfam database...	0.44	0.36	0.54	13	5127	11	2	9	0	23
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	0	0	0

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Performance of McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

Total Base Pair Counts
Total TP	1608
Total TN	2714514
Total FP	1361
Total FP CONTRA	133
Total FP INCONS	1137
Total FP COMP	91
Total FN	2255

Total Scores
MCC	0.482
Average MCC ± 95% Confidence Intervals	0.649 ± 0.064
Sensitivity	0.416
Positive Predictive Value	0.559
Nr of predictions	92

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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	-	0.59	0.53	0.68	21	5120	13	3	7	3	19
2KX8_A	7SK links to Rfam database...	0.88	0.83	0.94	15	845	1	0	1	0	3
2KXM_A	-	0.70	0.50	1.00	5	346	0	0	0	0	5
2KZL_A	-	0.86	0.74	1.00	14	1471	1	0	0	1	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L2K_A	-	0.97	0.95	1.00	18	843	0	0	0	0	1
2L3C_B	-	0.94	0.88	1.00	15	546	0	0	0	0	2
2L3E_A	-	1.00	1.00	1.00	13	582	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	0.89	0.79	1.00	27	2458	0	0	0	0	7
2L5Z_A	-	0.86	0.75	1.00	9	316	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LBS_A	-	1.00	1.00	1.00	14	482	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2LDL_A	-	0.73	0.55	1.00	6	345	0	0	0	0	5
2LDT_A	-	0.68	0.47	1.00	7	458	0	0	0	0	8
2LHP_A	-	1.00	1.00	1.00	16	650	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	8	343	2	0	0	2	0
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.51	0.46	0.58	18	6074	13	2	11	0	21
2LQZ_A	-	0.91	0.91	0.91	10	340	1	1	0	0	1
2LWK_A	-	0.83	0.77	0.91	10	485	2	0	1	1	3
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.31	0.30	0.33	6	4542	25	1	11	13	14
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.27	0.24	0.32	10	5120	21	0	21	0	32
2Y8W_B	-	1.00	1.00	1.00	6	184	2	0	0	2	0
2Y9C_V	-	0.59	0.54	0.65	13	2258	8	1	6	1	11
2YIE_X	-	0.36	0.33	0.40	4	1368	6	2	4	0	8
2YIE_Z	-	0.43	0.42	0.45	5	1529	6	3	3	0	7
3AKZ_H	tRNA links to Rfam database...	0.68	0.61	0.77	17	2679	6	1	4	1	11
3AM1_B	-	0.91	0.83	1.00	29	3211	1	0	0	1	6
3AMU_B	tRNA links to Rfam database...	0.75	0.59	0.94	16	2986	3	0	1	2	11
3IYQ_A	tmRNA links to Rfam database...	0.28	0.31	0.26	29	60614	87	19	64	4	65
3IZ4_A	tmRNA links to Rfam database...	0.42	0.36	0.49	47	70780	53	6	43	4	85
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	6867	6	0	6	0	24
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_1	-	0.65	0.47	0.90	9	1215	3	0	1	2	10
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_2	-	0.26	0.24	0.30	8	6189	21	0	19	2	25
3J0L_7	-	-0.01	0.00	0.00	0	1215	10	0	10	0	17
3J0L_a	-	0.26	0.19	0.38	3	1120	5	1	4	0	13
3J0L_h	-	0.65	0.49	0.88	21	6081	3	0	3	0	22
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.46	0.39	0.54	249	1116304	216	8	204	4	384
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3J2C_M	-	0.31	0.25	0.38	51	106357	86	12	71	3	156
3J2C_O	-	0.53	0.43	0.66	27	10255	15	1	13	1	36
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.43	0.72	23	7843	11	0	9	2	30
3NDB_M	-	0.81	0.70	0.93	43	9134	4	1	2	1	18
3NKB_B	-	0.36	0.31	0.44	8	1998	10	1	9	0	18
3NMU_E	-	0.41	0.17	1.00	1	560	3	0	0	3	5
3NPB_A	SAM links to Rfam database...	0.81	0.67	0.97	31	6989	4	1	0	3	15
3O58_2	5S_rRNA links to Rfam database...	0.83	0.71	0.96	27	7232	2	0	1	1	11
3O58_3	5_8S_rRNA links to Rfam database...	0.26	0.26	0.26	9	12368	26	10	16	0	26
3OVB_D	-	1.00	1.00	1.00	11	584	1	0	0	1	0
3OVS_D	-	0.96	0.92	1.00	12	549	0	0	0	0	1
3P22_G	-	0.96	0.92	1.00	11	730	0	0	0	0	1
3PDR_A	ykoK links to Rfam database...	0.69	0.56	0.87	40	12834	9	0	6	3	32
3R4F_A	-	0.96	0.92	1.00	23	2122	1	0	0	1	2
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.71	0.60	0.86	25	3887	4	0	4	0	17
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	0	5
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3TRZ_Z	-	0.91	0.83	1.00	5	205	2	0	0	2	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.73	0.57	0.95	21	3138	1	0	1	0	16
3UZL_B	tRNA links to Rfam database...	0.45	0.41	0.52	15	3541	14	0	14	0	22
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.44	0.38	0.54	15	4725	14	0	13	1	25
3ZEX_E	-	0.00	0.00	0.00	0	21894	53	4	47	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.69	0.53	0.90	26	6992	3	1	2	0	23
3ZEX_F	-	0.00	0.00	0.00	0	2619	9	2	7	0	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.27	0.21	0.34	11	14164	24	2	19	3	41
3ZEX_H	-	0.21	0.21	0.22	8	9009	29	6	22	1	30
3ZEX_B	-	0.11	0.09	0.13	53	1071960	373	32	335	6	505
3ZEX_G	-	0.31	0.27	0.36	20	16416	38	1	34	3	54
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	33	5	23	5	28
4A1C_3	5S_rRNA links to Rfam database...	0.25	0.22	0.29	12	7099	29	1	28	0	42
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4ATO_G	-	-0.01	0.00	0.00	0	523	5	0	5	0	10
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4
4FNJ_A	-	-0.02	0.00	0.00	0	588	7	0	7	0	16
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.66	1.00	21	3465	0	0	0	0	11
4FRN_A	AdoCbl-variant links to Rfam database...	0.73	0.56	0.95	20	5130	1	1	0	0	16
4HXH_A	-	1.00	1.00	1.00	6	319	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 ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

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

Performance of McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

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