CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Fold		RNAwolf
MCC	0.549	>	0.436
Average MCC ± 95% Confidence Intervals	0.642 ± 0.088	>	0.538 ± 0.088
Sensitivity	0.582	>	0.446
Positive Predictive Value	0.520	>	0.428
Total TP	1204	>	923
Total TN	975786	<	975948
Total FP	1397	<	1465
Total FP CONTRA	303	<	328
Total FP INCONS	810	<	904
Total FP COMP	284	>	233
Total FN	865	<	1146
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

Total Base Pair Counts
Total TP	1204
Total TN	975786
Total FP	1397
Total FP CONTRA	303
Total FP INCONS	810
Total FP COMP	284
Total FN	865

Total Scores
MCC	0.549
Average MCC ± 95% Confidence Intervals	0.642 ± 0.088
Sensitivity	0.582
Positive Predictive Value	0.520
Nr of predictions	69

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2. Individual counts for Fold [ 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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
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	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	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	-	0.90	0.90	0.90	26	2411	10	0	3	7	3
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LU0_A	-	0.93	0.88	1.00	14	424	0	0	0	0	2
2LWK_A	-	1.00	1.00	1.00	11	196	1	0	0	1	0
2M58_A	-	-0.02	0.00	0.00	0	529	15	0	15	0	12
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
2YIE_X	-	0.39	0.43	0.38	3	536	8	1	4	3	4
3AMU_B	tRNA links to Rfam database...	0.73	0.79	0.68	15	1135	10	0	7	3	4
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.15	0.18	0.17	2	399	11	4	6	1	9
3J0L_1	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_h	-	0.93	0.88	1.00	28	2112	2	0	0	2	4
3J0L_7	-	-0.02	0.00	0.00	0	507	12	2	10	0	10
3J0L_2	-	0.30	0.31	0.31	8	2224	25	2	16	7	18
3J16_L	tRNA links to Rfam database...	0.76	0.76	0.76	16	1138	5	0	5	0	5
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.55	0.58	0.53	239	421918	270	31	180	59	173
3J2C_O	-	0.71	0.76	0.67	31	3941	21	5	10	6	10
3J2C_M	-	0.23	0.27	0.20	26	39796	116	31	72	13	70
3J2L_3	5S_rRNA links to Rfam database...	0.80	0.82	0.78	28	2984	12	1	7	4	6
3J3D_C	tRNA links to Rfam database...	0.47	0.53	0.43	10	945	13	5	8	0	9
3J3E_7	5S_rRNA links to Rfam database...	0.59	0.59	0.61	20	2708	15	2	11	2	14
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2719	34	5	18	11	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.32	0.42	0.25	8	4729	41	12	12	17	11
3J3F_7	5S_rRNA links to Rfam database...	0.94	0.94	0.94	34	2898	4	1	1	2	2
3J3V_B	5S_rRNA links to Rfam database...	0.74	0.78	0.70	21	2626	17	2	7	8	6
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...	0.68	0.69	0.69	20	1504	9	4	5	0	9
3SIU_F	-	1.00	1.00	1.00	8	137	0	0	0	0	0
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	1	0	0	1	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	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
3UZL_B	tRNA links to Rfam database...	1.00	1.00	1.00	16	1277	8	0	0	8	0
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.94	0.91	0.97	30	1958	2	0	1	1	3
3ZEX_H	-	0.26	0.37	0.19	7	3588	30	19	11	0	12
3ZEX_F	-	-0.01	0.00	0.00	0	908	11	2	4	5	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.28	0.34	0.23	10	5330	46	9	25	12	19
3ZEX_G	-	0.98	0.96	1.00	43	6464	17	0	0	17	2
3ZEX_E	-	-0.01	0.00	0.00	0	8249	57	20	35	2	34
3ZEX_D	5S_rRNA links to Rfam database...	0.90	0.86	0.94	30	2764	8	0	2	6	5
3ZEX_B	-	0.32	0.36	0.29	123	420926	346	87	216	43	223
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...	0.86	0.84	0.89	31	2728	7	0	4	3	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4482	43	11	18	14	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ATO_G	-	0.38	0.43	0.38	3	212	5	5	0	0	4
4ENB_A	crcB links to Rfam database...	0.37	0.33	0.45	5	461	7	0	6	1	10
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	8	0	7	1	10
4FNJ_A	-	0.91	0.83	1.00	10	240	0	0	0	0	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.22	0.25	0.23	6	1176	20	7	13	0	18
4FRN_A	AdoCbl-variant links to Rfam database...	0.46	0.46	0.46	13	1820	15	7	8	0	15
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5
4JRC_A	-	0.34	0.35	0.35	6	605	11	0	11	0	11

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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	923
Total TN	975948
Total FP	1465
Total FP CONTRA	328
Total FP INCONS	904
Total FP COMP	233
Total FN	1146

Total Scores
MCC	0.436
Average MCC ± 95% Confidence Intervals	0.538 ± 0.088
Sensitivity	0.446
Positive Predictive Value	0.428
Nr of predictions	69

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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
2LI4_A	-	0.96	0.93	1.00	13	176	0	0	0	0	1
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_Z	-	0.62	0.63	0.63	5	594	7	1	2	4	3
2YIE_X	-	-0.01	0.00	0.00	0	536	11	1	7	3	7
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3J0L_g	-	-0.02	0.00	0.00	0	171	7	4	1	2	2
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_2	-	0.14	0.15	0.15	4	2223	26	4	19	3	22
3J16_L	tRNA links to Rfam database...	0.58	0.57	0.60	12	1139	9	2	6	1	9
3J20_1	tRNA links to Rfam database...	0.53	0.55	0.52	11	1091	11	4	6	1	9
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	2	9	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_7	5S_rRNA links to Rfam database...	0.57	0.56	0.59	19	2709	15	1	12	2	15
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2719	37	6	17	14	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 Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

2. Individual counts for Fold [ 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 ]