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		RNAsubopt
MCC	0.587	>	0.561
Average MCC ± 95% Confidence Intervals	0.662 ± 0.083	>	0.653 ± 0.083
Sensitivity	0.439	<	0.493
Positive Predictive Value	0.789	>	0.642
Total TP	677	<	760
Total TN	271688	>	271363
Total FP	213	<	475
Total FP CONTRA	16	<	40
Total FP INCONS	165	<	383
Total FP COMP	32	<	52
Total FN	865	>	782
P-value	3.56938820447e-08

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Performance plots

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

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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	677
Total TN	271688
Total FP	213
Total FP CONTRA	16
Total FP INCONS	165
Total FP COMP	32
Total FN	865

Total Scores
MCC	0.587
Average MCC ± 95% Confidence Intervals	0.662 ± 0.083
Sensitivity	0.439
Positive Predictive Value	0.789
Nr of predictions	56

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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
2L94_A	HIV_FE links to Rfam database...	0.92	0.90	0.95	18	971	1	0	1	0	2
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
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
2LWK_A	-	0.83	0.77	0.91	10	485	1	0	1	0	3
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
2Y9C_V	-	0.20	0.04	1.00	1	2277	0	0	0	0	23
2YIE_Z	-	0.82	0.67	1.00	8	1532	0	0	0	0	4
2YIE_X	-	0.76	0.58	1.00	7	1371	0	0	0	0	5
3AMU_B	tRNA links to Rfam database...	0.82	0.70	0.95	19	2983	3	0	1	2	8
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_1	-	0.65	0.47	0.90	9	1215	2	0	1	1	10
3J0L_h	-	0.76	0.63	0.93	27	6076	4	0	2	2	16
3J0L_7	-	0.60	0.41	0.88	7	1217	1	0	1	0	10
3J0L_g	-	0.00	0.00	0.00	0	465	0	0	0	0	4
3J0L_a	-	-0.01	0.00	0.00	0	1125	3	0	3	0	16
3J0L_2	-	0.49	0.24	1.00	8	6208	0	0	0	0	25
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_O	-	0.00	0.00	0.00	0	10296	0	0	0	0	63
3J2C_M	-	0.37	0.16	0.83	34	106450	8	0	7	1	173
3J2L_3	5S_rRNA links to Rfam database...	0.73	0.62	0.87	33	7837	7	0	5	2	20
3NMU_E	-	0.41	0.17	1.00	1	560	3	0	0	3	5
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
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
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.18	5	11753	29	5	18	6	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	7104	6	0	6	0	24
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

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Performance of RNAsubopt - scored lower in this pairwise comparison

1. Total counts & total scores for RNAsubopt

Total Base Pair Counts
Total TP	760
Total TN	271363
Total FP	475
Total FP CONTRA	40
Total FP INCONS	383
Total FP COMP	52
Total FN	782

Total Scores
MCC	0.561
Average MCC ± 95% Confidence Intervals	0.653 ± 0.083
Sensitivity	0.493
Positive Predictive Value	0.642
Nr of predictions	56

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LA5_A	-	0.39	0.26	0.63	5	622	3	1	2	0	14
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	1525	15	2	13	0	20
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
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
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	-	0.81	0.77	0.86	30	6070	9	0	5	4	9
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.83	0.77	0.91	10	485	1	0	1	0	3
2RRC_A	-	0.83	0.70	1.00	7	224	0	0	0	0	3
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
2Y9C_V	-	0.66	0.63	0.71	15	2257	8	1	5	2	9
2YIE_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
2YIE_X	-	0.82	0.67	1.00	8	1370	3	0	0	3	4
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_1	-	0.76	0.63	0.92	12	1212	2	0	1	1	7
3J0L_h	-	0.75	0.60	0.93	26	6077	4	0	2	2	17
3J0L_7	-	-0.01	0.00	0.00	0	1213	12	0	12	0	17
3J0L_g	-	-0.01	0.00	0.00	0	460	5	1	4	0	4
3J0L_a	-	0.35	0.31	0.42	5	1116	7	1	6	0	11
3J0L_2	-	0.25	0.24	0.28	8	6187	25	0	21	4	25
3J16_L	tRNA links to Rfam database...	0.41	0.37	0.48	11	2752	12	1	11	0	19
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	2	0	0	2	2
3J20_0	tRNA links to Rfam database...	0.43	0.40	0.48	12	2825	14	0	13	1	18
3J2C_O	-	0.56	0.49	0.65	31	10248	17	1	16	0	32
3J2C_M	-	0.44	0.37	0.52	76	106346	72	8	61	3	131
3J2L_3	5S_rRNA links to Rfam database...	0.61	0.53	0.72	28	7836	13	0	11	2	25
3NMU_E	-	0.54	0.50	0.60	3	556	5	0	2	3	3
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
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...	0.61	0.50	0.75	21	3888	7	1	6	0	21
3SIU_F	-	0.85	0.73	1.00	8	370	0	0	0	0	3
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...	0.48	0.38	0.61	14	3547	9	0	9	0	23
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.87	0.78	0.97	31	4721	2	0	1	1	9
3ZEX_E	-	0.00	0.00	0.00	0	21893	54	4	48	2	77
3ZEX_G	-	0.46	0.42	0.52	31	16411	32	3	26	3	43
3ZEX_D	5S_rRNA links to Rfam database...	0.80	0.69	0.92	34	6984	3	0	3	0	15
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.13	5	11742	43	5	29	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.52	0.43	0.64	18	4343	11	2	8	1	24
4ENB_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1314	7	0	7	0	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.32	0.28	0.38	9	3462	15	0	15	0	23
4FRN_A	AdoCbl-variant links to Rfam database...	0.51	0.44	0.59	16	5124	11	3	8	0	20
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	0	0	0

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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 RNAsubopt - scored lower in this pairwise comparison

1. Total counts & total scores for RNAsubopt

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