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	0.503	>	0.433
Average MCC ± 95% Confidence Intervals	0.644 ± 0.083	>	0.532 ± 0.088
Sensitivity	0.517	>	0.443
Positive Predictive Value	0.491	>	0.425
Total TP	1062	>	910
Total TN	975750	<	975772
Total FP	1302	<	1465
Total FP CONTRA	295	<	328
Total FP INCONS	807	<	904
Total FP COMP	200	<	233
Total FN	993	<	1145
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	1062
Total TN	975750
Total FP	1302
Total FP CONTRA	295
Total FP INCONS	807
Total FP COMP	200
Total FN	993

Total Scores
MCC	0.503
Average MCC ± 95% Confidence Intervals	0.644 ± 0.083
Sensitivity	0.517
Positive Predictive Value	0.491
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	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
2LU0_A	-	0.93	0.88	1.00	14	424	1	0	0	1	2
2LWK_A	-	0.95	0.91	1.00	10	197	2	0	0	2	1
2M58_A	-	0.60	0.58	0.64	7	533	5	1	3	1	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
3AMU_B	tRNA links to Rfam database...	0.86	0.79	0.94	15	1141	4	0	1	3	4
3J0L_2	-	0.29	0.31	0.30	8	2223	21	1	18	2	18
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
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
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	0.56	0.55	231	421948	234	41	148	45	181
3J2C_O	-	0.62	0.61	0.64	25	3948	17	3	11	3	16
3J2C_M	-	0.38	0.44	0.34	42	39801	95	33	49	13	54
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.68	0.74	23	2989	11	0	8	3	11
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2718	36	8	16	12	15
3J3E_7	5S_rRNA links to Rfam database...	0.61	0.59	0.65	20	2710	14	2	9	3	14
3J3F_8	5_8S_rRNA links to Rfam database...	0.31	0.42	0.23	8	4726	41	12	15	14	11
3J3F_7	5S_rRNA links to Rfam database...	0.21	0.22	0.22	8	2897	29	3	26	0	28
3J3V_B	5S_rRNA links to Rfam database...	0.65	0.59	0.73	16	2634	10	0	6	4	11
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
3UZL_B	tRNA links to Rfam database...	0.62	0.75	0.52	12	1270	17	8	3	6	4
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W1K_J	tRNA-Sec links to Rfam database...	0.86	0.77	0.96	24	1653	1	1	0	0	7
3W3S_B	tRNA-Sec links to Rfam database...	0.49	0.45	0.54	15	1961	14	1	12	1	18
3ZEX_H	-	0.27	0.37	0.21	7	3591	30	14	13	3	12
3ZEX_F	-	0.00	0.00	0.00	0	910	9	0	4	5	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.33	0.34	0.32	10	5343	25	4	17	4	19
3ZEX_G	-	0.36	0.40	0.34	18	6454	40	11	24	5	27
3ZEX_E	-	0.00	0.00	0.00	0	8256	53	17	31	5	34
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.66	0.88	23	2770	6	1	2	3	12
3ZEX_B	-	0.12	0.14	0.12	47	420944	379	78	283	18	299
3ZND_W	tRNA links to Rfam database...	0.24	0.38	0.16	3	1172	25	9	7	9	5
4A1C_3	5S_rRNA links to Rfam database...	0.28	0.30	0.28	11	2724	30	4	24	2	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	33	11	16	6	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ATO_G	-	-0.03	0.00	0.00	0	215	5	0	5	0	7
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
4FNJ_A	-	-0.04	0.00	0.00	0	243	7	0	7	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	0.93	0.88	1.00	21	1181	0	0	0	0	3
4FRN_A	AdoCbl-variant links to Rfam database...	0.82	0.71	0.95	20	1827	1	1	0	0	8
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0
4JF2_A	preQ1-II links to Rfam database...	0.92	1.00	0.86	24	1054	5	4	0	1	0
4JRC_A	-	0.97	0.94	1.00	16	606	0	0	0	0	1

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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	910
Total TN	975772
Total FP	1465
Total FP CONTRA	328
Total FP INCONS	904
Total FP COMP	233
Total FN	1145

Total Scores
MCC	0.433
Average MCC ± 95% Confidence Intervals	0.532 ± 0.088
Sensitivity	0.443
Positive Predictive Value	0.425
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	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.52	0.50	0.56	9	512	7	0	7	0	9
2LDL_A	-	0.88	0.78	1.00	7	133	0	0	0	0	2
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	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	-	0.84	0.79	0.88	23	2414	11	0	3	8	6
2LQZ_A	-	1.00	1.00	1.00	8	124	1	0	0	1	0
2LU0_A	-	0.97	0.94	1.00	15	423	0	0	0	0	1
2LWK_A	-	0.48	0.45	0.56	5	198	5	0	4	1	6
2M58_A	-	0.60	0.58	0.64	7	533	4	1	3	0	5
2YIE_X	-	-0.01	0.00	0.00	0	536	11	1	7	3	7
2YIE_Z	-	0.62	0.63	0.63	5	594	7	1	2	4	3
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3J0L_2	-	0.14	0.15	0.15	4	2223	26	4	19	3	22
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.14	0.18	0.14	2	397	13	4	8	1	9
3J0L_1	-	0.68	0.54	0.88	7	476	5	0	1	4	6
3J0L_h	-	0.47	0.41	0.57	13	2117	12	1	9	2	19
3J0L_7	-	-0.02	0.00	0.00	0	509	10	1	9	0	10
3J0L_g	-	-0.02	0.00	0.00	0	171	7	4	1	2	2
3J16_L	tRNA links to Rfam database...	0.58	0.57	0.60	12	1139	9	2	6	1	9
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	2	9	1	9
3J20_1	tRNA links to Rfam database...	0.53	0.55	0.52	11	1091	11	4	6	1	9
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.55	0.55	0.56	228	421959	243	27	154	62	184
3J2C_O	-	0.41	0.44	0.40	18	3942	30	7	20	3	23
3J2C_M	-	0.21	0.25	0.19	24	39797	113	35	69	9	72
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.71	0.73	24	2987	13	1	8	4	10
3J3D_C	tRNA links to Rfam database...	0.92	0.95	0.90	18	948	3	2	0	1	1
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2719	37	6	17	14	15
3J3E_7	5S_rRNA links to Rfam database...	0.57	0.56	0.59	19	2709	15	1	12	2	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.28	0.37	0.23	7	4730	39	9	15	15	12
3J3F_7	5S_rRNA links to Rfam database...	0.27	0.28	0.28	10	2898	27	4	22	1	26
3J3V_B	5S_rRNA links to Rfam database...	0.59	0.59	0.59	16	2629	16	1	10	5	11
3RKF_A	Purine links to Rfam database...	0.89	0.83	0.95	20	845	1	0	1	0	4
3SD1_A	THF links to Rfam database...	0.58	0.59	0.59	17	1504	12	2	10	0	12
3SIU_F	-	0.86	0.75	1.00	6	139	0	0	0	0	2
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	0	0	0	0	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	-0.05	0.00	0.00	0	103	6	0	5	1	5
3U4M_B	-	0.50	0.50	0.52	11	1255	12	1	9	2	11
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	7	0	0	7	2
3VJR_D	-	1.00	1.00	1.00	12	239	1	0	0	1	0
3W1K_J	tRNA-Sec links to Rfam database...	0.81	0.77	0.86	24	1650	5	0	4	1	7
3W3S_B	tRNA-Sec links to Rfam database...	0.70	0.70	0.72	23	1957	10	0	9	1	10
3ZEX_H	-	-0.01	0.00	0.00	0	3593	33	17	15	1	19
3ZEX_F	-	0.00	0.00	0.00	0	910	17	0	4	13	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.08	0.10	0.07	3	5328	43	18	25	0	26
3ZEX_G	-	0.20	0.20	0.21	9	6465	37	13	20	4	36
3ZEX_E	-	-0.01	0.00	0.00	0	8244	60	23	37	0	34
3ZEX_D	5S_rRNA links to Rfam database...	0.26	0.26	0.27	9	2763	24	8	16	0	26
3ZEX_B	-	0.18	0.19	0.17	65	420964	343	98	225	20	281
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	15	0	4	11	2
4A1C_3	5S_rRNA links to Rfam database...	0.32	0.30	0.35	11	2732	21	1	19	1	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.12	0.15	0.10	3	4487	38	12	14	12	17
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.26	0.24	0.30	7	1414	17	2	14	1	22
4ATO_G	-	-0.03	0.00	0.00	0	213	7	4	3	0	7
4ENB_A	crcB links to Rfam database...	0.45	0.40	0.55	6	461	5	1	4	0	9
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	9	0	8	1	10
4FNJ_A	-	-0.04	0.00	0.00	0	243	7	0	7	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	0.54	0.50	0.60	12	1182	8	3	5	0	12
4FRN_A	AdoCbl-variant links to Rfam database...	-0.01	0.00	0.00	0	1828	20	1	19	0	28
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0
4JF2_A	preQ1-II links to Rfam database...	0.72	0.67	0.80	16	1062	4	4	0	0	8
4JRC_A	-	0.71	0.65	0.79	11	608	3	2	1	0	6

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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 ]