CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CentroidHomfold‑LAST		RNAwolf
MCC	0.574	>	0.400
Average MCC ± 95% Confidence Intervals	0.639 ± 0.081	>	0.521 ± 0.085
Sensitivity	0.439	>	0.372
Positive Predictive Value	0.755	>	0.437
Total TP	797	>	676
Total TN	320183	>	319690
Total FP	301	<	945
Total FP CONTRA	23	<	93
Total FP INCONS	235	<	779
Total FP COMP	43	<	73
Total FN	1018	<	1139
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of CentroidHomfold-LAST 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 CentroidHomfold‑LAST 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 CentroidHomfold‑LAST and RNAwolf).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidHomfold-LAST 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 CentroidHomfold‑LAST and RNAwolf).

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Performance of CentroidHomfold‑LAST - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidHomfold‑LAST

Total Base Pair Counts
Total TP	797
Total TN	320183
Total FP	301
Total FP CONTRA	23
Total FP INCONS	235
Total FP COMP	43
Total FN	1018

Total Scores
MCC	0.574
Average MCC ± 95% Confidence Intervals	0.639 ± 0.081
Sensitivity	0.439
Positive Predictive Value	0.755
Nr of predictions	60

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2. Individual counts for CentroidHomfold‑LAST [ 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	1529	11	0	11	0	20
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LDT_A	-	0.72	0.53	1.00	8	457	0	0	0	0	7
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
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	-	0.00	0.00	0.00	0	6101	4	0	4	0	39
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LU0_A	-	0.93	0.88	1.00	14	1162	0	0	0	0	2
2LWK_A	-	0.83	0.77	0.91	10	485	1	0	1	0	3
2M58_A	-	-0.01	0.00	0.00	0	1648	5	0	5	0	17
2YIE_X	-	0.76	0.58	1.00	7	1371	0	0	0	0	5
2YIE_Z	-	0.82	0.67	1.00	8	1532	0	0	0	0	4
3AMU_B	tRNA links to Rfam database...	0.82	0.70	0.95	19	2983	3	0	1	2	8
3J0L_7	-	0.60	0.41	0.88	7	1217	1	0	1	0	10
3J0L_2	-	0.49	0.24	1.00	8	6208	0	0	0	0	25
3J0L_g	-	0.00	0.00	0.00	0	465	0	0	0	0	4
3J0L_h	-	0.76	0.63	0.93	27	6076	4	0	2	2	16
3J0L_1	-	0.65	0.47	0.90	9	1215	2	0	1	1	10
3J0L_a	-	-0.01	0.00	0.00	0	1125	3	0	3	0	16
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.35	0.37	0.34	11	2818	22	3	18	1	19
3J2C_M	-	0.37	0.16	0.83	34	106450	8	0	7	1	173
3J2C_O	-	0.00	0.00	0.00	0	10296	0	0	0	0	63
3J2L_3	5S_rRNA links to Rfam database...	0.73	0.62	0.87	33	7837	7	0	5	2	20
3J3D_C	tRNA links to Rfam database...	0.68	0.61	0.77	17	2753	5	0	5	0	11
3J3E_7	5S_rRNA links to Rfam database...	0.64	0.54	0.76	29	7102	9	0	9	0	25
3J3E_8	5_8S_rRNA links to Rfam database...	0.05	0.03	0.08	1	7490	16	1	11	4	32
3J3F_7	5S_rRNA links to Rfam database...	0.65	0.58	0.74	29	7221	10	1	9	0	21
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.33	0.33	12	12210	33	4	20	9	24
3J3V_B	5S_rRNA links to Rfam database...	0.51	0.37	0.72	21	6992	8	1	7	0	36
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.64	0.45	0.90	19	3895	2	0	2	0	23
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	0	5
3SN2_B	IRE_II links to Rfam database...	0.91	0.83	1.00	10	396	0	0	0	0	2
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	-	0.58	0.43	0.80	16	3140	4	0	4	0	21
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.85	0.73	1.00	29	4724	1	0	0	1	11
3ZEX_E	-	0.00	0.00	0.00	0	21914	33	1	30	2	77
3ZEX_G	-	0.75	0.61	0.92	45	16422	7	0	4	3	29
3ZEX_D	5S_rRNA links to Rfam database...	0.75	0.65	0.86	32	6984	5	0	5	0	17
3ZND_W	tRNA links to Rfam database...	0.47	0.39	0.56	9	2987	10	0	7	3	14
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	7104	6	0	6	0	24
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.18	5	11753	29	5	18	6	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.71	0.50	1.00	21	4350	1	0	0	1	21
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...	0.76	0.58	1.00	11	1315	0	0	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.41	0.41	0.43	13	3456	17	3	14	0	19
4FRN_A	AdoCbl-variant links to Rfam database...	0.36	0.39	0.34	14	5110	27	3	24	0	22
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	0	0	0
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12
4JRC_A	-	0.75	0.57	1.00	13	1527	0	0	0	0	10

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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	676
Total TN	319690
Total FP	945
Total FP CONTRA	93
Total FP INCONS	779
Total FP COMP	73
Total FN	1139

Total Scores
MCC	0.400
Average MCC ± 95% Confidence Intervals	0.521 ± 0.085
Sensitivity	0.372
Positive Predictive Value	0.437
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
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_7	-	-0.01	0.00	0.00	0	1214	11	0	11	0	17
3J0L_2	-	0.11	0.12	0.11	4	6181	34	5	26	3	29
3J0L_g	-	0.16	0.25	0.11	1	456	8	6	2	0	3
3J0L_h	-	0.33	0.30	0.37	13	6070	24	0	22	2	30
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_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
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_M	-	0.19	0.17	0.21	35	106323	133	11	122	0	172
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_7	5S_rRNA links to Rfam database...	0.41	0.35	0.49	19	7101	20	1	19	0	35
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7470	42	4	29	9	33
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_E	-	0.00	0.00	0.00	0	21876	69	10	59	0	77
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
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
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
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 CentroidHomfold‑LAST - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidHomfold‑LAST

2. Individual counts for CentroidHomfold‑LAST [ 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 ]