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		RNAwolf
MCC	0.420	>	0.353
Average MCC ± 95% Confidence Intervals	0.580 ± 0.079	>	0.479 ± 0.083
Sensitivity	0.357	>	0.328
Positive Predictive Value	0.495	>	0.382
Total TP	1133	>	1040
Total TN	2539270	>	2538840
Total FP	1231	<	1777
Total FP CONTRA	104	<	192
Total FP INCONS	1054	<	1489
Total FP COMP	73	<	96
Total FN	2039	<	2132
P-value	3.56938820447e-08

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Performance plots

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

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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	1133
Total TN	2539270
Total FP	1231
Total FP CONTRA	104
Total FP INCONS	1054
Total FP COMP	73
Total FN	2039

Total Scores
MCC	0.420
Average MCC ± 95% Confidence Intervals	0.580 ± 0.079
Sensitivity	0.357
Positive Predictive Value	0.495
Nr of predictions	68

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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
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
2LU0_A	-	0.93	0.88	1.00	14	1162	1	0	0	1	2
2LWK_A	-	0.83	0.77	0.91	10	485	2	0	1	1	3
2M58_A	-	0.56	0.47	0.67	8	1641	4	1	3	0	9
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
3AMU_B	tRNA links to Rfam database...	0.75	0.59	0.94	16	2986	3	0	1	2	11
3J0L_2	-	0.26	0.24	0.30	8	6189	21	0	19	2	25
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_1	-	0.65	0.47	0.90	9	1215	3	0	1	2	10
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
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	1	4	1	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
3J2C_O	-	0.53	0.43	0.66	27	10255	15	1	13	1	36
3J2C_M	-	0.31	0.25	0.38	51	106357	86	12	71	3	156
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.43	0.72	23	7843	11	0	9	2	30
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7479	36	3	21	12	33
3J3E_7	5S_rRNA links to Rfam database...	0.46	0.37	0.59	20	7106	14	1	13	0	34
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.31	0.30	11	12209	38	4	22	12	25
3J3F_7	5S_rRNA links to Rfam database...	0.18	0.16	0.22	8	7223	29	1	28	0	42
3J3V_B	5S_rRNA links to Rfam database...	0.49	0.33	0.73	19	6995	7	0	7	0	38
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
3W1K_J	tRNA-Sec links to Rfam database...	0.78	0.63	0.96	24	4161	1	1	0	0	14
3W3S_B	tRNA-Sec links to Rfam database...	0.44	0.38	0.54	15	4725	14	0	13	1	25
3ZEX_H	-	0.21	0.21	0.22	8	9009	29	6	22	1	30
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_G	-	0.31	0.27	0.36	20	16416	38	1	34	3	54
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_B	-	0.11	0.09	0.13	53	1071960	373	32	335	6	505
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
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
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
4JF2_A	preQ1-II links to Rfam database...	0.83	0.81	0.86	25	2821	4	3	1	0	6
4JRC_A	-	0.83	0.70	1.00	16	1524	0	0	0	0	7

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Performance of RNAwolf - scored lower in this pairwise comparison

1. Total counts & total scores for RNAwolf

Total Base Pair Counts
Total TP	1040
Total TN	2538840
Total FP	1777
Total FP CONTRA	192
Total FP INCONS	1489
Total FP COMP	96
Total FN	2132

Total Scores
MCC	0.353
Average MCC ± 95% Confidence Intervals	0.479 ± 0.083
Sensitivity	0.328
Positive Predictive Value	0.382
Nr of predictions	68

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.52	0.50	0.56	10	1522	8	0	8	0	10
2LDL_A	-	0.74	0.64	0.88	7	343	1	0	1	0	4
2LDT_A	-	0.86	0.80	0.92	12	452	1	0	1	0	3
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	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	10	266	0	0	0	0	0
2LKR_A	-	0.81	0.74	0.88	29	6072	8	0	4	4	10
2LQZ_A	-	0.91	0.91	0.91	10	340	1	1	0	0	1
2LU0_A	-	0.97	0.94	1.00	15	1161	3	0	0	3	1
2LWK_A	-	0.37	0.38	0.38	5	483	9	0	8	1	8
2M58_A	-	0.51	0.47	0.57	8	1639	6	3	3	0	9
2YIE_X	-	-0.01	0.00	0.00	0	1364	15	4	10	1	12
2YIE_Z	-	0.43	0.42	0.45	5	1529	9	1	5	3	7
3AMU_B	tRNA links to Rfam database...	0.68	0.63	0.74	17	2980	9	0	6	3	10
3J0L_2	-	0.11	0.12	0.11	4	6181	34	5	26	3	29
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.18	0.19	0.20	3	1113	12	1	11	0	13
3J0L_1	-	0.68	0.63	0.75	12	1209	5	0	4	1	7
3J0L_h	-	0.33	0.30	0.37	13	6070	24	0	22	2	30
3J0L_7	-	-0.01	0.00	0.00	0	1214	11	0	11	0	17
3J0L_g	-	0.16	0.25	0.11	1	456	8	6	2	0	3
3J16_L	tRNA links to Rfam database...	0.45	0.40	0.52	12	2752	11	0	11	0	18
3J20_0	tRNA links to Rfam database...	0.40	0.40	0.41	12	2821	18	0	17	1	18
3J20_1	tRNA links to Rfam database...	0.46	0.52	0.41	12	2897	17	6	11	0	11
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.45	0.42	0.49	266	1116224	283	17	258	8	367
3J2C_O	-	0.40	0.37	0.44	23	10244	30	0	29	1	40
3J2C_M	-	0.19	0.17	0.21	35	106323	133	11	122	0	172
3J2L_3	5S_rRNA links to Rfam database...	0.55	0.49	0.62	26	7833	18	0	16	2	27
3J3D_C	tRNA links to Rfam database...	0.79	0.75	0.84	21	2750	5	2	2	1	7
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7470	42	4	29	9	33
3J3E_7	5S_rRNA links to Rfam database...	0.41	0.35	0.49	19	7101	20	1	19	0	35
3J3F_8	5_8S_rRNA links to Rfam database...	0.23	0.25	0.21	9	12204	45	5	28	12	27
3J3F_7	5S_rRNA links to Rfam database...	0.21	0.20	0.23	10	7216	34	2	32	0	40
3J3V_B	5S_rRNA links to Rfam database...	0.43	0.37	0.51	21	6980	20	2	18	0	36
3RKF_A	Purine links to Rfam database...	0.72	0.62	0.84	21	2186	4	0	4	0	13
3SD1_A	THF links to Rfam database...	0.46	0.43	0.50	18	3880	18	0	18	0	24
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	0	0	0	0	1
3TS0_U	-	1.00	1.00	1.00	6	247	2	0	0	2	0
3TS2_V	-	-0.02	0.00	0.00	0	270	7	0	6	1	5
3U4M_B	-	0.44	0.38	0.52	14	3133	13	0	13	0	23
3UZL_B	tRNA links to Rfam database...	0.72	0.59	0.88	22	3545	4	1	2	1	15
3VJR_D	-	1.00	1.00	1.00	13	617	1	0	0	1	0
3W1K_J	tRNA-Sec links to Rfam database...	0.71	0.66	0.78	25	4154	7	0	7	0	13
3W3S_B	tRNA-Sec links to Rfam database...	0.68	0.63	0.74	25	4719	10	0	9	1	15
3ZEX_H	-	0.00	0.00	0.00	0	9006	40	8	31	1	38
3ZEX_F	-	-0.01	0.00	0.00	0	2613	20	6	9	5	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.05	0.06	0.06	3	14144	49	12	37	0	49
3ZEX_G	-	0.20	0.18	0.23	13	16415	43	6	37	0	61
3ZEX_E	-	0.00	0.00	0.00	0	21876	69	10	59	0	77
3ZEX_D	5S_rRNA links to Rfam database...	0.20	0.18	0.22	9	6980	32	3	29	0	40
3ZEX_B	-	0.14	0.13	0.15	70	1071902	417	55	353	9	488
3ZND_W	tRNA links to Rfam database...	0.50	0.48	0.52	11	2982	13	0	10	3	12
4A1C_3	5S_rRNA links to Rfam database...	0.23	0.20	0.28	11	7101	28	2	26	0	43
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.09	0.08	3	11741	46	10	27	9	30
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.23	0.19	0.30	8	4344	20	1	18	1	34
4ATO_G	-	-0.02	0.00	0.00	0	520	8	1	7	0	10
4ENB_A	crcB links to Rfam database...	0.35	0.32	0.40	6	1260	9	1	8	0	13
4ENC_A	crcB links to Rfam database...	0.34	0.32	0.38	6	1310	10	1	9	0	13
4FNJ_A	-	-0.02	0.00	0.00	0	587	8	0	8	0	16
4FRG_B	AdoCbl-variant links to Rfam database...	0.56	0.50	0.64	16	3461	10	1	8	1	16
4FRN_A	AdoCbl-variant links to Rfam database...	-0.01	0.00	0.00	0	5119	32	0	32	0	36
4HXH_A	-	1.00	1.00	1.00	6	319	2	0	0	2	0
4JF2_A	preQ1-II links to Rfam database...	0.67	0.58	0.78	18	2827	5	3	2	0	13
4JRC_A	-	0.58	0.52	0.67	12	1522	6	0	6	0	11

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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 McQFold - scored higher in this pairwise comparison

1. Total counts & total scores for McQFold

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

Performance of RNAwolf - scored lower in this pairwise comparison

1. Total counts & total scores for RNAwolf

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