CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ContextFold		MCFold
MCC	0.449	>	0.290
Average MCC ± 95% Confidence Intervals	0.520 ± 0.083	>	0.295 ± 0.081
Sensitivity	0.402	>	0.320
Positive Predictive Value	0.511	>	0.276
Total TP	394	>	313
Total TN	106722	>	106359
Total FP	383	<	871
Total FP CONTRA	35	<	116
Total FP INCONS	342	<	705
Total FP COMP	6	<	50
Total FN	585	<	666
P-value	3.56938820447e-08

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Performance plots

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

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Performance of ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

Total Base Pair Counts
Total TP	394
Total TN	106722
Total FP	383
Total FP CONTRA	35
Total FP INCONS	342
Total FP COMP	6
Total FN	585

Total Scores
MCC	0.449
Average MCC ± 95% Confidence Intervals	0.520 ± 0.083
Sensitivity	0.402
Positive Predictive Value	0.511
Nr of predictions	48

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2. Individual counts for ContextFold [ 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	5	0	5	0	9
PDB_00018	-	0.22	0.20	0.27	4	1020	11	2	9	0	16
PDB_00020	-	0.41	0.35	0.50	7	766	7	0	7	0	13
PDB_00041	-	0.70	0.50	1.00	6	624	0	0	0	0	6
PDB_00053	-	0.73	0.55	1.00	6	429	0	0	0	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	4151	35	0	35	0	36
PDB_00124	-	0.70	0.50	1.00	5	491	0	0	0	0	5
PDB_00128	-	0.75	0.57	1.00	8	488	0	0	0	0	6
PDB_00134	-	0.57	0.50	0.67	4	372	2	0	2	0	4
PDB_00138	-	-0.02	0.00	0.00	0	372	6	1	5	0	8
PDB_00209	-	0.67	0.45	1.00	5	556	0	0	0	0	6
PDB_00243	-	0.50	0.42	0.63	5	622	3	0	3	0	7
PDB_00352	-	0.92	0.84	1.00	16	1209	0	0	0	0	3
PDB_00571	tRNA links to Rfam database...	0.85	0.76	0.95	19	3301	1	1	0	0	6
PDB_00713	-	0.42	0.38	0.47	8	1999	9	0	9	0	13
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2687	14	0	14	0	23
PDB_00828	Purine links to Rfam database...	0.86	0.74	1.00	20	2465	0	0	0	0	7
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_00842	-	0.72	0.63	0.83	5	372	1	0	1	0	3
PDB_00851	-	0.45	0.39	0.53	16	4723	14	0	14	0	25
PDB_00857	-	0.67	0.60	0.75	9	1069	3	0	3	0	6
PDB_00874	-	-0.02	0.00	0.00	0	929	17	0	17	0	20
PDB_00886	-	-0.01	0.00	0.00	0	4151	35	0	35	0	40
PDB_00918	-	0.67	0.57	0.80	4	320	1	0	1	0	3
PDB_01009	tRNA links to Rfam database...	0.90	0.90	0.90	19	2464	3	0	2	1	2
PDB_01020	Purine links to Rfam database...	0.86	0.74	1.00	17	2261	1	0	0	1	6
PDB_01040	-	0.30	0.30	0.33	6	1110	12	0	12	0	14
PDB_01059	-	0.75	0.57	1.00	4	227	0	0	0	0	3
PDB_01070	-	0.17	0.15	0.21	8	12682	30	0	30	0	46
PDB_01073	SAM links to Rfam database...	0.48	0.44	0.54	15	4343	13	2	11	0	19
PDB_01194	-	0.77	0.60	1.00	9	487	0	0	0	0	6
PDB_01201	-	0.53	0.41	0.69	9	1115	4	0	4	0	13
PDB_01203	-	0.77	0.68	0.87	13	1161	2	2	0	0	6
PDB_01250	-	0.22	0.20	0.24	8	12057	26	3	22	1	33
PDB_01260	-	0.52	0.36	0.75	9	1818	3	0	3	0	16
PDB_01281	-	-0.03	0.00	0.00	0	366	12	0	12	0	14
PDB_01299	-	0.73	0.60	0.90	9	893	3	1	0	2	6
PDB_01309	-	-0.01	0.00	0.00	0	9120	60	9	51	0	39
RFA_00636	HDV_ribozyme links to Rfam database...	0.52	0.43	0.63	12	3986	7	0	7	0	16
RFA_00767	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1875	6	3	3	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	1876	5	2	3	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	4	4	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	2001	5	2	3	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1937	6	1	5	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	1938	5	2	3	0	8
RFA_00808	RydC links to Rfam database...	0.58	0.44	0.78	7	2007	2	0	2	0	9
RFA_00809	RydC links to Rfam database...	0.39	0.31	0.50	5	2135	6	0	5	1	11

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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 ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

2. Individual counts for ContextFold [ 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 ]