CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAwolf		MCFold
MCC	0.376	>	0.290
Average MCC ± 95% Confidence Intervals	0.408 ± 0.086	>	0.295 ± 0.081
Sensitivity	0.364	>	0.320
Positive Predictive Value	0.400	>	0.276
Total TP	356	>	313
Total TN	106604	>	106359
Total FP	557	<	871
Total FP CONTRA	77	<	116
Total FP INCONS	456	<	705
Total FP COMP	24	<	50
Total FN	623	<	666
P-value	3.56938820447e-08

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Performance plots

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

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Performance of RNAwolf - scored higher in this pairwise comparison

1. Total counts & total scores for RNAwolf

Total Base Pair Counts
Total TP	356
Total TN	106604
Total FP	557
Total FP CONTRA	77
Total FP INCONS	456
Total FP COMP	24
Total FN	623

Total Scores
MCC	0.376
Average MCC ± 95% Confidence Intervals	0.408 ± 0.086
Sensitivity	0.364
Positive Predictive Value	0.400
Nr of predictions	48

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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
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.42	0.36	0.50	5	936	6	0	5	1	9
PDB_00018	-	0.18	0.15	0.25	3	1023	9	2	7	0	17
PDB_00020	-	0.39	0.35	0.47	7	765	8	0	8	0	13
PDB_00041	-	0.61	0.50	0.75	6	622	2	0	2	0	6
PDB_00053	-	0.73	0.55	1.00	6	429	0	0	0	0	5
PDB_00056	-	-0.02	0.00	0.00	0	615	15	0	15	0	16
PDB_00123	-	0.31	0.33	0.30	12	4146	28	4	24	0	24
PDB_00124	-	-0.02	0.00	0.00	0	485	11	2	9	0	10
PDB_00128	-	0.84	0.71	1.00	10	486	0	0	0	0	4
PDB_00134	-	0.72	0.63	0.83	5	372	3	0	1	2	3
PDB_00138	-	-0.02	0.00	0.00	0	371	7	0	7	0	8
PDB_00209	-	0.74	0.55	1.00	6	555	0	0	0	0	5
PDB_00243	-	0.54	0.42	0.71	5	623	2	0	2	0	7
PDB_00352	-	0.67	0.58	0.79	11	1211	3	0	3	0	8
PDB_00571	tRNA links to Rfam database...	0.89	0.84	0.95	21	3299	2	1	0	1	4
PDB_00713	-	0.28	0.24	0.33	5	2001	11	0	10	1	16
PDB_00716	HDV_ribozyme links to Rfam database...	0.68	0.57	0.81	13	2685	3	0	3	0	10
PDB_00828	Purine links to Rfam database...	0.85	0.81	0.88	22	2460	3	1	2	0	5
PDB_00829	Purine links to Rfam database...	0.78	0.75	0.82	18	2256	4	1	3	0	6
PDB_00842	-	0.72	0.63	0.83	5	372	1	0	1	0	3
PDB_00851	-	0.34	0.34	0.35	14	4713	26	0	26	0	27
PDB_00857	-	0.57	0.60	0.56	9	1065	7	0	7	0	6
PDB_00874	-	-0.02	0.00	0.00	0	928	18	0	18	0	20
PDB_00886	-	-0.01	0.00	0.00	0	4143	43	4	39	0	40
PDB_00918	-	-0.02	0.00	0.00	0	317	8	0	8	0	7
PDB_01009	tRNA links to Rfam database...	0.45	0.52	0.39	11	2457	18	6	11	1	10
PDB_01020	Purine links to Rfam database...	0.84	0.83	0.86	19	2256	5	1	2	2	4
PDB_01040	-	0.24	0.25	0.25	5	1108	15	1	14	0	15
PDB_01059	-	-0.03	0.00	0.00	0	226	5	1	4	0	7
PDB_01070	-	0.00	0.00	0.00	0	12665	55	8	47	0	54
PDB_01073	SAM links to Rfam database...	0.17	0.18	0.17	6	4336	29	3	26	0	28
PDB_01194	-	0.61	0.53	0.73	8	485	3	0	3	0	7
PDB_01201	-	0.75	0.68	0.83	15	1110	3	0	3	0	7
PDB_01203	-	-0.01	0.00	0.00	0	1165	11	0	11	0	19
PDB_01250	-	0.45	0.44	0.46	18	12051	21	11	10	0	23
PDB_01260	-	-0.01	0.00	0.00	0	1809	21	0	21	0	25
PDB_01281	-	-0.04	0.00	0.00	0	365	13	0	13	0	14
PDB_01299	-	0.65	0.53	0.80	8	893	2	0	2	0	7
PDB_01309	-	0.26	0.31	0.22	12	9126	42	14	28	0	27
RFA_00636	HDV_ribozyme links to Rfam database...	0.40	0.39	0.41	11	3978	19	1	15	3	17
RFA_00767	Corona_pk3 links to Rfam database...	0.48	0.44	0.53	8	1876	8	1	6	1	10
RFA_00768	Corona_pk3 links to Rfam database...	0.50	0.44	0.57	8	1877	8	1	5	2	10
RFA_00769	Corona_pk3 links to Rfam database...	0.41	0.44	0.38	8	1932	13	3	10	0	10
RFA_00770	Corona_pk3 links to Rfam database...	0.51	0.50	0.53	9	1999	12	2	6	4	9
RFA_00773	Corona_pk3 links to Rfam database...	0.42	0.39	0.47	7	1938	12	1	7	4	11
RFA_00779	Corona_pk3 links to Rfam database...	0.26	0.28	0.26	5	1934	14	6	8	0	13
RFA_00808	RydC links to Rfam database...	0.68	0.56	0.82	9	2005	2	2	0	0	7
RFA_00809	RydC links to Rfam database...	0.47	0.38	0.60	6	2135	6	0	4	2	10

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Performance of MCFold - scored lower in this pairwise comparison

1. Total counts & total scores for MCFold

Total Base Pair Counts
Total TP	313
Total TN	106359
Total FP	871
Total FP CONTRA	116
Total FP INCONS	705
Total FP COMP	50
Total FN	666

Total Scores
MCC	0.290
Average MCC ± 95% Confidence Intervals	0.295 ± 0.081
Sensitivity	0.320
Positive Predictive Value	0.276
Nr of predictions	48

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.76	0.79	0.73	11	931	6	2	2	2	3
PDB_00018	-	0.18	0.20	0.19	4	1014	17	2	15	0	16
PDB_00020	-	0.35	0.35	0.39	7	762	11	0	11	0	13
PDB_00041	-	0.23	0.25	0.23	3	617	12	0	10	2	9
PDB_00053	-	0.56	0.55	0.60	6	425	4	0	4	0	5
PDB_00056	-	0.93	0.88	1.00	14	616	0	0	0	0	2
PDB_00123	-	-0.01	0.00	0.00	0	4143	43	4	39	0	36
PDB_00124	-	-0.02	0.00	0.00	0	484	12	2	10	0	10
PDB_00128	-	0.77	0.71	0.83	10	484	2	0	2	0	4
PDB_00134	-	0.58	0.63	0.56	5	369	5	1	3	1	3
PDB_00138	-	-0.02	0.00	0.00	0	369	11	0	9	2	8
PDB_00209	-	-0.02	0.00	0.00	0	550	11	2	9	0	11
PDB_00243	-	-0.02	0.00	0.00	0	615	15	1	14	0	12
PDB_00352	-	0.18	0.21	0.18	4	1203	18	1	17	0	15
PDB_00571	tRNA links to Rfam database...	-0.01	0.00	0.00	0	3287	34	3	31	0	25
PDB_00713	-	0.21	0.24	0.21	5	1992	20	1	18	1	16
PDB_00716	HDV_ribozyme links to Rfam database...	0.22	0.26	0.19	6	2670	25	5	20	0	17
PDB_00828	Purine links to Rfam database...	0.34	0.37	0.33	10	2455	22	1	19	2	17
PDB_00829	Purine links to Rfam database...	0.25	0.29	0.23	7	2248	23	6	17	0	17
PDB_00842	-	-0.02	0.00	0.00	0	369	10	0	9	1	8
PDB_00851	-	0.23	0.24	0.24	10	4711	32	0	32	0	31
PDB_00857	-	-0.02	0.00	0.00	0	1062	19	6	13	0	15
PDB_00874	-	-0.02	0.00	0.00	0	926	20	0	20	0	20
PDB_00886	-	-0.01	0.00	0.00	0	4143	43	4	39	0	40
PDB_00918	-	-0.02	0.00	0.00	0	317	10	0	8	2	7
PDB_01009	tRNA links to Rfam database...	0.43	0.52	0.35	11	2454	21	5	15	1	10
PDB_01020	Purine links to Rfam database...	0.29	0.30	0.29	7	2254	20	2	15	3	16
PDB_01040	-	0.28	0.30	0.29	6	1107	15	2	13	0	14
PDB_01059	-	-0.03	0.00	0.00	0	223	8	2	6	0	7
PDB_01070	-	0.68	0.70	0.66	38	12662	22	2	18	2	16
PDB_01073	SAM links to Rfam database...	0.52	0.56	0.49	19	4332	22	1	19	2	15
PDB_01194	-	0.66	0.60	0.75	9	484	3	0	3	0	6
PDB_01201	-	0.75	0.68	0.83	15	1110	3	0	3	0	7
PDB_01203	-	0.73	0.74	0.74	14	1157	5	4	1	0	5
PDB_01250	-	0.00	0.00	0.00	0	12036	54	18	36	0	41
PDB_01260	-	0.55	0.56	0.56	14	1805	11	1	10	0	11
PDB_01281	-	-0.04	0.00	0.00	0	365	13	0	13	0	14
PDB_01299	-	0.66	0.67	0.67	10	888	7	1	4	2	5
PDB_01309	-	-0.01	0.00	0.00	0	9122	58	9	49	0	39
RFA_00636	HDV_ribozyme links to Rfam database...	0.36	0.39	0.34	11	3973	29	0	21	8	17
RFA_00767	Corona_pk3 links to Rfam database...	0.36	0.44	0.31	8	1865	19	3	15	1	10
RFA_00768	Corona_pk3 links to Rfam database...	0.36	0.44	0.31	8	1865	19	3	15	1	10
RFA_00769	Corona_pk3 links to Rfam database...	0.45	0.50	0.41	9	1931	18	2	11	5	9
RFA_00770	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1992	29	2	22	5	18
RFA_00773	Corona_pk3 links to Rfam database...	0.43	0.50	0.38	9	1929	16	4	11	1	9
RFA_00779	Corona_pk3 links to Rfam database...	0.45	0.56	0.37	10	1926	17	7	10	0	8
RFA_00808	RydC links to Rfam database...	0.39	0.44	0.35	7	1996	19	1	12	6	9
RFA_00809	RydC links to Rfam database...	0.30	0.38	0.25	6	2121	18	6	12	0	10

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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 RNAwolf - scored higher in this pairwise comparison

1. Total counts & total scores for RNAwolf

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

Performance of MCFold - scored lower in this pairwise comparison

1. Total counts & total scores for MCFold

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