CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Vsfold4		RNAwolf
MCC	0.466	>	0.439
Average MCC ± 95% Confidence Intervals	0.558 ± 0.081	>	0.534 ± 0.086
Sensitivity	0.388	<	0.411
Positive Predictive Value	0.568	>	0.478
Total TP	620	<	656
Total TN	209529	>	209249
Total FP	520	<	788
Total FP CONTRA	37	<	83
Total FP INCONS	434	<	632
Total FP COMP	49	<	73
Total FN	978	>	942
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Vsfold4 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 Vsfold4 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 Vsfold4 and RNAwolf).
Comparison of average Matthews Correlation Coefficients (MCCs) for Vsfold4 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 Vsfold4 and RNAwolf).

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Performance of Vsfold4 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold4

Total Base Pair Counts
Total TP	620
Total TN	209529
Total FP	520
Total FP CONTRA	37
Total FP INCONS	434
Total FP COMP	49
Total FN	978

Total Scores
MCC	0.466
Average MCC ± 95% Confidence Intervals	0.558 ± 0.081
Sensitivity	0.388
Positive Predictive Value	0.568
Nr of predictions	60

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2. Individual counts for Vsfold4 [ 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...	-0.01	0.00	0.00	0	1527	13	0	13	0	20
2LDL_A	-	0.85	0.73	1.00	8	343	1	0	0	1	3
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
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
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	-	0.31	0.28	0.34	11	6073	21	3	18	0	28
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LU0_A	-	0.69	0.63	0.77	10	1163	3	0	3	0	6
2LWK_A	-	0.83	0.77	0.91	10	485	1	0	1	0	3
2M58_A	-	-0.01	0.00	0.00	0	1647	6	0	6	0	17
2YIE_X	-	0.36	0.33	0.40	4	1368	6	2	4	0	8
2YIE_Z	-	-0.01	0.00	0.00	0	1529	11	3	8	0	12
3AMU_B	tRNA links to Rfam database...	0.64	0.56	0.75	15	2983	7	0	5	2	12
3J0L_h	-	0.38	0.28	0.52	12	6082	11	0	11	0	31
3J0L_7	-	0.51	0.41	0.64	7	1214	4	0	4	0	10
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_8	-	0.70	0.50	1.00	4	186	0	0	0	0	4
3J0L_1	-	0.28	0.21	0.40	4	1215	6	1	5	0	15
3J0L_a	-	0.39	0.31	0.50	5	1118	5	2	3	0	11
3J0L_2	-	0.38	0.36	0.41	12	6187	18	3	14	1	21
3J16_L	tRNA links to Rfam database...	0.82	0.67	1.00	20	2755	0	0	0	0	10
3J20_1	tRNA links to Rfam database...	0.71	0.70	0.73	16	2904	6	0	6	0	7
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J2C_O	-	0.30	0.24	0.39	15	10258	24	0	23	1	48
3J2L_3	5S_rRNA links to Rfam database...	0.57	0.45	0.73	24	7842	12	1	8	3	29
3J3D_C	tRNA links to Rfam database...	0.44	0.39	0.50	11	2753	11	1	10	0	17
3J3E_8	5_8S_rRNA links to Rfam database...	0.07	0.06	0.09	2	7481	32	2	18	12	31
3J3E_7	5S_rRNA links to Rfam database...	0.48	0.35	0.66	19	7111	10	0	10	0	35
3J3F_7	5S_rRNA links to Rfam database...	0.21	0.18	0.26	9	7226	25	0	25	0	41
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.31	0.37	11	12216	27	4	15	8	25
3J3V_B	5S_rRNA links to Rfam database...	0.17	0.12	0.24	7	6992	22	1	21	0	50
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...	0.19	0.17	0.24	7	3887	22	1	21	0	35
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	1	0	0	1	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	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.53	0.41	0.71	15	3549	6	1	5	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...	0.67	0.58	0.79	23	4724	7	0	6	1	17
3ZEX_G	-	0.30	0.23	0.39	17	16427	27	2	25	0	57
3ZEX_D	5S_rRNA links to Rfam database...	0.55	0.45	0.69	22	6989	10	0	10	0	27
3ZEX_E	-	0.08	0.06	0.11	5	21900	40	1	39	0	72
3ZND_W	tRNA links to Rfam database...	0.41	0.39	0.43	9	2982	14	2	10	2	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.28	0.24	0.33	8	11757	28	0	16	12	25
4A1C_3	5S_rRNA links to Rfam database...	0.26	0.22	0.32	12	7103	25	2	23	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	-	0.32	0.30	0.38	3	520	5	1	4	0	7
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1317	0	0	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.56	0.47	0.68	15	3464	7	1	6	0	17
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	0	0	0
4JF2_A	preQ1-II links to Rfam database...	0.66	0.52	0.84	16	2831	3	0	3	0	15
4JRC_A	-	0.29	0.22	0.42	5	1528	7	0	7	0	18

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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	656
Total TN	209249
Total FP	788
Total FP CONTRA	83
Total FP INCONS	632
Total FP COMP	73
Total FN	942

Total Scores
MCC	0.439
Average MCC ± 95% Confidence Intervals	0.534 ± 0.086
Sensitivity	0.411
Positive Predictive Value	0.478
Nr of predictions	60

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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
2LI4_A	-	0.97	0.94	1.00	15	481	0	0	0	0	1
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_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
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_1	-	0.68	0.63	0.75	12	1209	5	0	4	1	7
3J0L_a	-	0.18	0.19	0.20	3	1113	12	1	11	0	13
3J0L_2	-	0.11	0.12	0.11	4	6181	34	5	26	3	29
3J16_L	tRNA links to Rfam database...	0.45	0.40	0.52	12	2752	11	0	11	0	18
3J20_1	tRNA links to Rfam database...	0.46	0.52	0.41	12	2897	17	6	11	0	11
3J20_0	tRNA links to Rfam database...	0.40	0.40	0.41	12	2821	18	0	17	1	18
3J2C_O	-	0.40	0.37	0.44	23	10244	30	0	29	1	40
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_7	5S_rRNA links to Rfam database...	0.21	0.20	0.23	10	7216	34	2	32	0	40
3J3F_8	5_8S_rRNA links to Rfam database...	0.23	0.25	0.21	9	12204	45	5	28	12	27
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
3W3S_B	tRNA-Sec links to Rfam database...	0.68	0.63	0.74	25	4719	10	0	9	1	15
3ZEX_G	-	0.20	0.18	0.23	13	16415	43	6	37	0	61
3ZEX_D	5S_rRNA links to Rfam database...	0.20	0.18	0.22	9	6980	32	3	29	0	40
3ZEX_E	-	0.00	0.00	0.00	0	21876	69	10	59	0	77
3ZND_W	tRNA links to Rfam database...	0.50	0.48	0.52	11	2982	13	0	10	3	12
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.09	0.08	3	11741	46	10	27	9	30
4A1C_3	5S_rRNA links to Rfam database...	0.23	0.20	0.28	11	7101	28	2	26	0	43
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.56	0.50	0.64	16	3461	10	1	8	1	16
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 Vsfold4 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold4

2. Individual counts for Vsfold4 [ 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 ]