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	0.661	>	0.575
Average MCC ± 95% Confidence Intervals	0.699 ± 0.056	>	0.640 ± 0.066
Sensitivity	0.573	<	0.595
Positive Predictive Value	0.769	>	0.563
Total TP	1302	<	1353
Total TN	233130	>	232421
Total FP	466	<	1236
Total FP CONTRA	61	<	142
Total FP INCONS	330	<	907
Total FP COMP	75	<	187
Total FN	972	>	921
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	1302
Total TN	233130
Total FP	466
Total FP CONTRA	61
Total FP INCONS	330
Total FP COMP	75
Total FN	972

Total Scores
MCC	0.661
Average MCC ± 95% Confidence Intervals	0.699 ± 0.056
Sensitivity	0.573
Positive Predictive Value	0.769
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	-	0.60	0.36	1.00	4	402	0	0	0	0	7
2K63_A	-	0.95	0.90	1.00	9	397	0	0	0	0	1
2K66_A	-	0.95	0.90	1.00	9	222	0	0	0	0	1
2KD8_A	-	1.00	1.00	1.00	9	222	1	0	0	1	0
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KE6_A	K10_TLS links to Rfam database...	0.89	0.79	1.00	15	1113	1	0	0	1	4
2KEZ_A	-	0.89	0.80	1.00	8	268	0	0	0	0	2
2KFC_A	-	0.49	0.25	1.00	5	625	0	0	0	0	15
2KGP_A	-	0.81	0.67	1.00	6	294	1	0	0	1	3
2KMJ_A	-	1.00	1.00	1.00	11	367	1	0	0	1	0
2KPV_A	-	0.96	0.92	1.00	12	549	0	0	0	0	1
2KU0_A	-	0.75	0.56	1.00	9	694	0	0	0	0	7
2KUR_A	K10_TLS links to Rfam database...	0.87	0.76	1.00	16	1112	0	0	0	0	5
2KUU_A	K10_TLS links to Rfam database...	0.84	0.71	1.00	15	1113	1	0	0	1	6
2KUV_A	K10_TLS links to Rfam database...	0.85	0.73	1.00	16	1112	0	0	0	0	6
2KUW_A	K10_TLS links to Rfam database...	0.87	0.76	1.00	16	1112	0	0	0	0	5
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
2RP0_A	-	0.64	0.42	1.00	5	346	0	0	0	0	7
2RPT_A	-	1.00	1.00	1.00	7	183	0	0	0	0	0
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WW9_F	-	0.71	0.60	0.86	6	293	1	0	1	0	4
2WW9_E	-	-0.01	0.00	0.00	0	556	5	0	5	0	14
2WW9_D	-	0.32	0.23	0.46	6	1940	7	2	5	0	20
2WWQ_V	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	28
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
2ZY6_A	-	0.58	0.58	0.58	7	691	5	1	4	0	5
2ZZN_D	tRNA links to Rfam database...	0.84	0.78	0.91	21	2462	2	0	2	0	6
3A2K_C	tRNA links to Rfam database...	0.86	0.75	1.00	21	2905	0	0	0	0	7
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
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
3DW4_A	-	-0.02	0.00	0.00	0	348	3	0	3	0	10
3GCA_A	-	0.54	0.29	1.00	5	523	0	0	0	0	12
3GX2_A	SAM links to Rfam database...	0.47	0.40	0.57	16	4343	13	1	11	1	24
3HAY_E	-	0.91	0.83	1.00	15	2263	3	0	0	3	3
3HJW_D	-	0.88	0.83	0.94	15	1637	3	0	1	2	3
3IAB_R	-	0.92	0.86	1.00	12	1023	0	0	0	0	2
3ID5_D	-	0.49	0.33	0.75	3	492	6	0	1	5	6
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.20	0.18	0.24	6	4253	19	2	17	0	27
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	6867	6	0	6	0	24
3J0L_1	-	0.65	0.47	0.90	9	1215	3	0	1	2	10
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
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
3J0L_7	-	-0.01	0.00	0.00	0	1215	10	0	10	0	17
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
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2830	20	0	20	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.20	0.21	0.19	7	12210	33	8	21	4	26
3JYX_3	5S_rRNA links to Rfam database...	0.21	0.22	0.20	6	6298	24	9	15	0	21
3KTW_C	-	0.36	0.30	0.45	13	4531	17	1	15	1	30
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
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
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
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
4A1C_3	5S_rRNA links to Rfam database...	0.25	0.22	0.29	12	7099	29	1	28	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	33	5	23	5	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
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

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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	1353
Total TN	232421
Total FP	1236
Total FP CONTRA	142
Total FP INCONS	907
Total FP COMP	187
Total FN	921

Total Scores
MCC	0.575
Average MCC ± 95% Confidence Intervals	0.640 ± 0.066
Sensitivity	0.595
Positive Predictive Value	0.563
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	395	1	0	0	1	0
2K63_A	-	0.90	0.90	0.90	9	396	4	0	1	3	1
2K66_A	-	1.00	1.00	1.00	10	221	0	0	0	0	0
2KD8_A	-	1.00	1.00	1.00	9	222	1	0	0	1	0
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	1	0	0	1	1
2KE6_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	1109	2	0	0	2	0
2KEZ_A	-	0.90	0.90	0.90	9	266	1	0	1	0	1
2KFC_A	-	0.28	0.25	0.36	5	616	9	2	7	0	15
2KGP_A	-	1.00	1.00	1.00	9	291	1	0	0	1	0
2KMJ_A	-	1.00	1.00	1.00	11	367	1	0	0	1	0
2KPV_A	-	1.00	1.00	1.00	13	548	2	0	0	2	0
2KU0_A	-	0.97	0.94	1.00	15	688	0	0	0	0	1
2KUR_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	21	1107	0	0	0	0	0
2KUU_A	K10_TLS links to Rfam database...	0.98	0.95	1.00	20	1108	1	0	0	1	1
2KUV_A	K10_TLS links to Rfam database...	0.98	0.95	1.00	21	1107	0	0	0	0	1
2KUW_A	K10_TLS links to Rfam database...	0.95	0.95	0.95	20	1107	1	0	1	0	1
2KX8_A	7SK links to Rfam database...	0.91	0.89	0.94	16	844	2	0	1	1	2
2KXM_A	-	1.00	1.00	1.00	10	341	1	0	0	1	0
2KZL_A	-	0.80	0.84	0.76	16	1464	9	1	4	4	3
2L1F_B	Gammaretro_CES links to Rfam database...	0.73	0.76	0.70	19	2118	9	0	8	1	6
2L1F_A	Gammaretro_CES links to Rfam database...	0.72	0.75	0.69	18	2054	9	0	8	1	6
2L2K_A	-	1.00	1.00	1.00	19	842	1	0	0	1	0
2L3C_B	-	0.97	0.94	1.00	16	545	0	0	0	0	1
2L3E_A	-	1.00	1.00	1.00	13	582	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	1.00	1.00	1.00	34	2451	0	0	0	0	0
2L5Z_A	-	0.96	0.92	1.00	11	314	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LA5_A	-	-0.03	0.00	0.00	0	615	15	0	15	0	19
2LBS_A	-	1.00	1.00	1.00	14	482	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.41	0.45	0.39	9	1517	16	0	14	2	11
2LDL_A	-	0.95	0.91	1.00	10	341	2	0	0	2	1
2LDT_A	-	0.75	0.73	0.79	11	451	3	0	3	0	4
2LHP_A	-	1.00	1.00	1.00	16	650	1	0	0	1	0
2LJJ_A	-	1.00	1.00	1.00	8	343	2	0	0	2	0
2LK3_A	-	1.00	1.00	1.00	10	266	0	0	0	0	0
2LKR_A	-	0.93	0.92	0.95	36	6067	14	0	2	12	3
2LQZ_A	-	0.91	0.91	0.91	10	340	1	1	0	0	1
2LWK_A	-	0.92	0.92	0.92	12	483	2	0	1	1	1
2RP0_A	-	0.44	0.42	0.50	5	341	5	1	4	0	7
2RPT_A	-	1.00	1.00	1.00	7	183	2	0	0	2	0
2RRC_A	-	0.95	0.90	1.00	9	222	0	0	0	0	1
2WRQ_Y	tRNA links to Rfam database...	0.27	0.35	0.22	6	2823	25	8	13	4	11
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WW9_E	-	-0.02	0.00	0.00	0	547	14	0	14	0	14
2WW9_D	-	-0.01	0.00	0.00	0	1925	28	5	23	0	26
2WWQ_V	tRNA links to Rfam database...	0.15	0.18	0.15	5	2892	30	4	25	1	23
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.20	0.25	0.17	5	4530	37	2	23	12	15
2XQD_Y	tRNA links to Rfam database...	0.34	0.37	0.32	10	2819	22	1	20	1	17
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.23	0.24	0.24	10	5110	32	1	30	1	32
2Y8W_B	-	1.00	1.00	1.00	6	184	2	0	0	2	0
2Y9C_V	-	0.62	0.67	0.59	16	2251	13	2	9	2	8
2YIE_X	-	0.06	0.08	0.06	1	1361	21	1	15	5	11
2YIE_Z	-	0.36	0.50	0.27	6	1518	18	4	12	2	6
2ZY6_A	-	0.51	0.58	0.47	7	688	8	3	5	0	5
2ZZN_D	tRNA links to Rfam database...	0.61	0.63	0.61	17	2457	13	1	10	2	10
3A2K_C	tRNA links to Rfam database...	0.44	0.46	0.42	13	2895	18	2	16	0	15
3A3A_A	tRNA-Sec links to Rfam database...	0.89	0.86	0.91	32	3620	3	1	2	0	5
3AKZ_H	tRNA links to Rfam database...	0.40	0.43	0.39	12	2670	19	3	16	0	16
3AM1_B	-	0.93	0.89	0.97	31	3208	2	0	1	1	4
3AMU_B	tRNA links to Rfam database...	0.44	0.48	0.42	13	2972	18	2	16	0	14
3DW4_A	-	0.90	0.90	0.90	9	341	3	0	1	2	1
3GCA_A	-	0.04	0.06	0.07	1	514	13	1	12	0	16
3GX2_A	SAM links to Rfam database...	0.47	0.48	0.48	19	4331	22	0	21	1	21
3HAY_E	-	1.00	1.00	1.00	18	2260	11	0	0	11	0
3HJW_D	-	0.94	0.94	0.94	17	1635	8	0	1	7	1
3IAB_R	-	0.84	0.93	0.76	13	1018	8	2	2	4	1
3ID5_D	-	0.34	0.33	0.38	3	488	9	0	5	4	6
3IVN_B	Purine links to Rfam database...	0.39	0.39	0.40	12	2316	18	0	18	0	19
3IWN_A	c-di-GMP-I links to Rfam database...	0.19	0.21	0.18	7	4238	33	8	25	0	26
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.69	0.74	37	6853	14	0	13	1	17
3J0L_1	-	0.79	0.79	0.79	15	1206	6	0	4	2	4
3J0L_8	-	1.00	1.00	1.00	8	182	0	0	0	0	0
3J0L_a	-	0.16	0.19	0.17	3	1110	15	1	14	0	13
3J0L_h	-	0.91	0.91	0.91	39	6062	13	0	4	9	4
3J0L_7	-	-0.01	0.00	0.00	0	1206	19	4	15	0	17
3J0L_g	-	0.13	0.25	0.08	1	452	12	8	4	0	3
3J0L_2	-	0.21	0.24	0.18	8	6172	39	7	29	3	25
3J16_L	tRNA links to Rfam database...	0.45	0.47	0.44	14	2743	19	1	17	1	16
3JYV_7	tRNA links to Rfam database...	0.21	0.22	0.21	7	2817	26	0	26	0	25
3JYX_4	5_8S_rRNA links to Rfam database...	0.20	0.24	0.17	8	12199	43	16	23	4	25
3JYX_3	5S_rRNA links to Rfam database...	0.41	0.52	0.33	14	6285	34	12	17	5	13
3KTW_C	-	0.40	0.40	0.43	17	4520	24	4	19	1	26
3LA5_A	Purine links to Rfam database...	0.32	0.32	0.34	11	2453	21	1	20	0	23
3NDB_M	-	0.23	0.23	0.24	14	9121	46	1	44	1	47
3NKB_B	-	0.56	0.58	0.56	15	1989	13	0	12	1	11
3NMU_E	-	0.28	0.33	0.25	2	553	12	0	6	6	4
3O58_2	5S_rRNA links to Rfam database...	0.20	0.24	0.17	9	7208	44	5	38	1	29
3O58_3	5_8S_rRNA links to Rfam database...	0.22	0.26	0.19	9	12355	45	9	30	6	26
3OVB_D	-	1.00	1.00	1.00	11	584	2	0	0	2	0
3OVS_D	-	1.00	1.00	1.00	13	548	0	0	0	0	0
3P22_G	-	1.00	1.00	1.00	12	729	5	0	0	5	0
3PDR_A	ykoK links to Rfam database...	0.66	0.61	0.72	44	12819	19	0	17	2	28
3R4F_A	-	0.92	0.92	0.92	23	2120	5	0	2	3	2
3R9X_C	-	0.69	0.70	0.70	7	585	7	0	3	4	3
3RKF_A	Purine links to Rfam database...	0.70	0.65	0.76	22	2182	7	1	6	0	12
3SD1_A	THF links to Rfam database...	0.33	0.33	0.35	14	3876	26	0	26	0	28
3SIU_F	-	0.42	0.45	0.42	5	366	7	1	6	0	6
3SN2_B	IRE_II links to Rfam database...	0.55	0.58	0.54	7	393	6	0	6	0	5
3TRZ_Z	-	-0.04	0.00	0.00	0	201	9	0	9	0	6
3TS0_U	-	1.00	1.00	1.00	6	247	2	0	0	2	0
3TS2_V	-	-0.02	0.00	0.00	0	268	9	0	8	1	5
3U4M_B	-	0.59	0.59	0.59	22	3123	15	0	15	0	15
3VJR_D	-	1.00	1.00	1.00	13	617	1	0	0	1	0
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.67	0.71	36	7089	17	1	14	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.11	5	11735	56	10	31	15	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4ENB_A	crcB links to Rfam database...	0.61	0.63	0.60	12	1255	8	2	6	0	7
4ENC_A	crcB links to Rfam database...	0.28	0.32	0.27	6	1304	17	2	14	1	13

^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 ]