CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNASampler(seed)		Pknots
MCC	0.455	>	0.446
Average MCC ± 95% Confidence Intervals	0.368 ± 0.078	<	0.421 ± 0.086
Sensitivity	0.284	<	0.429
Positive Predictive Value	0.738	>	0.475
Total TP	293	<	442
Total TN	100869	>	100336
Total FP	123	<	573
Total FP CONTRA	30	<	63
Total FP INCONS	74	<	425
Total FP COMP	19	<	85
Total FN	738	>	589
P-value	5.21379515797e-05

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Performance plots

Comparison of performance of RNASampler(seed) and Pknots. 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 RNASampler(seed) and Pknots).
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 RNASampler(seed) and Pknots).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASampler(seed) and Pknots. 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 RNASampler(seed) and Pknots).

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Performance of RNASampler(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for RNASampler(seed)

Total Base Pair Counts
Total TP	293
Total TN	100869
Total FP	123
Total FP CONTRA	30
Total FP INCONS	74
Total FP COMP	19
Total FN	738

Total Scores
MCC	0.455
Average MCC ± 95% Confidence Intervals	0.368 ± 0.078
Sensitivity	0.284
Positive Predictive Value	0.738
Nr of predictions	69

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2. Individual counts for RNASampler(seed) [ 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...	0.88	0.79	1.00	11	935	0	0	0	0	3
PDB_00012	mir-TAR links to Rfam database...	1.00	1.00	1.00	7	399	3	0	0	3	0
PDB_00553	mir-TAR links to Rfam database...	1.00	1.00	1.00	11	454	0	0	0	0	0
PDB_00716	HDV_ribozyme links to Rfam database...	0.50	0.39	0.64	9	2687	6	0	5	1	14
PDB_00810	s2m links to Rfam database...	0.42	0.18	1.00	3	1078	0	0	0	0	14
PDB_01050	UnaL2 links to Rfam database...	0.92	0.85	1.00	11	619	2	0	0	2	2
PDB_01051	Telomerase-cil links to Rfam database...	0.45	0.31	0.67	4	897	6	0	2	4	9
PDB_01152	HIV_FS2 links to Rfam database...	0.84	0.71	1.00	10	551	0	0	0	0	4
RFA_00390	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	0	0	0	0	15
RFA_00416	Hammerhead_3 links to Rfam database...	0.63	0.40	1.00	6	1479	1	0	0	1	9
RFA_00433	Hammerhead_3 links to Rfam database...	0.63	0.40	1.00	6	1425	1	0	0	1	9
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	5	0	0	5	0
RFA_00632	HDV_ribozyme links to Rfam database...	0.78	0.68	0.90	19	4074	2	1	1	0	9
RFA_00636	HDV_ribozyme links to Rfam database...	0.85	0.75	0.95	21	3983	1	1	0	0	7
RFA_00642	Vimentin3 links to Rfam database...	0.58	0.39	0.88	7	2918	1	0	1	0	11
RFA_00643	Vimentin3 links to Rfam database...	0.21	0.17	0.27	3	2200	8	0	8	0	15
RFA_00644	Vimentin3 links to Rfam database...	0.44	0.33	0.60	6	2691	4	1	3	0	12
RFA_00645	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2403	12	3	9	0	18
RFA_00649	Vimentin3 links to Rfam database...	0.44	0.33	0.60	6	2135	4	1	3	0	12
RFA_00651	Vimentin3 links to Rfam database...	0.33	0.22	0.50	4	2072	4	1	3	0	14
RFA_00653	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2133	12	3	9	0	18
RFA_00654	Vimentin3 links to Rfam database...	0.39	0.28	0.56	5	2406	4	1	3	0	13
RFA_00658	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00659	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00664	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00667	Hammerhead_1 links to Rfam database...	0.53	0.29	1.00	4	986	0	0	0	0	10
RFA_00668	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00672	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	13
RFA_00673	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00674	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00675	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00677	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00678	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	946	0	0	0	0	14
RFA_00680	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00684	Hammerhead_1 links to Rfam database...	0.53	0.29	1.00	4	986	0	0	0	0	10
RFA_00685	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00703	Hammerhead_1 links to Rfam database...	0.46	0.21	1.00	3	4275	0	0	0	0	11
RFA_00704	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	987	3	0	3	0	14
RFA_00705	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00706	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00707	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00708	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00709	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00710	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00711	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00715	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	946	0	0	0	0	14
RFA_00716	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	943	3	0	3	0	14
RFA_00717	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	14
RFA_00730	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00731	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00733	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00734	s2m links to Rfam database...	0.64	0.42	1.00	5	898	0	0	0	0	7
RFA_00736	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00737	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00745	s2m links to Rfam database...	0.50	0.25	1.00	3	943	0	0	0	0	9
RFA_00749	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00758	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00762	s2m links to Rfam database...	0.64	0.42	1.00	5	898	0	0	0	0	7
RFA_00763	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00764	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00765	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00767	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1878	3	3	0	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1878	3	3	0	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1937	6	1	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.52	0.39	0.70	7	2006	3	3	0	0	11
RFA_00773	Corona_pk3 links to Rfam database...	0.59	0.50	0.69	9	1940	4	4	0	0	9
RFA_00779	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1940	3	3	0	0	8
RFA_00808	RydC links to Rfam database...	0.58	0.56	0.60	9	2001	6	0	6	0	7
RFA_00809	RydC links to Rfam database...	0.36	0.38	0.35	6	2128	11	1	10	0	10

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Performance of Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

Total Base Pair Counts
Total TP	442
Total TN	100336
Total FP	573
Total FP CONTRA	63
Total FP INCONS	425
Total FP COMP	85
Total FN	589

Total Scores
MCC	0.446
Average MCC ± 95% Confidence Intervals	0.421 ± 0.086
Sensitivity	0.429
Positive Predictive Value	0.475
Nr of predictions	69

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2. Individual counts for Pknots [ 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...	1.00	1.00	1.00	14	932	0	0	0	0	0
PDB_00012	mir-TAR links to Rfam database...	1.00	1.00	1.00	7	399	3	0	0	3	0
PDB_00553	mir-TAR links to Rfam database...	1.00	1.00	1.00	11	454	0	0	0	0	0
PDB_00716	HDV_ribozyme links to Rfam database...	0.69	0.70	0.70	16	2678	8	0	7	1	7
PDB_00810	s2m links to Rfam database...	0.46	0.41	0.54	7	1068	6	2	4	0	10
PDB_01050	UnaL2 links to Rfam database...	0.92	0.85	1.00	11	619	2	0	0	2	2
PDB_01051	Telomerase-cil links to Rfam database...	0.31	0.31	0.33	4	891	9	1	7	1	9
PDB_01152	HIV_FS2 links to Rfam database...	0.88	0.79	1.00	11	550	0	0	0	0	3
RFA_00390	Hammerhead_3 links to Rfam database...	0.69	0.67	0.71	10	1417	6	0	4	2	5
RFA_00416	Hammerhead_3 links to Rfam database...	0.93	0.93	0.93	14	1470	5	0	1	4	1
RFA_00433	Hammerhead_3 links to Rfam database...	0.66	0.67	0.67	10	1416	7	0	5	2	5
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	13	0	0	13	0
RFA_00632	HDV_ribozyme links to Rfam database...	0.40	0.43	0.39	12	4064	19	4	15	0	16
RFA_00636	HDV_ribozyme links to Rfam database...	0.80	0.86	0.75	24	3973	8	6	2	0	4
RFA_00642	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2911	15	2	13	0	18
RFA_00643	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2196	15	1	14	0	18
RFA_00644	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2682	19	4	15	0	18
RFA_00645	Vimentin3 links to Rfam database...	0.18	0.17	0.20	3	2400	13	1	11	1	15
RFA_00649	Vimentin3 links to Rfam database...	0.48	0.50	0.47	9	2126	11	0	10	1	9
RFA_00651	Vimentin3 links to Rfam database...	0.53	0.50	0.56	9	2064	8	0	7	1	9
RFA_00653	Vimentin3 links to Rfam database...	0.33	0.33	0.33	6	2127	12	3	9	0	12
RFA_00654	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2397	18	7	11	0	18
RFA_00658	Hammerhead_1 links to Rfam database...	0.33	0.29	0.40	4	1118	8	0	6	2	10
RFA_00659	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1119	11	0	9	2	14
RFA_00664	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	980	11	0	10	1	14
RFA_00667	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	978	13	1	11	1	14
RFA_00668	Hammerhead_1 links to Rfam database...	0.46	0.43	0.50	6	978	7	0	6	1	8
RFA_00672	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	897	6	0	6	0	13
RFA_00673	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1120	9	0	8	1	14
RFA_00674	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1116	12	0	12	0	14
RFA_00675	Hammerhead_1 links to Rfam database...	0.29	0.29	0.31	4	977	9	1	8	0	10
RFA_00677	Hammerhead_1 links to Rfam database...	0.61	0.57	0.67	8	978	6	0	4	2	6
RFA_00678	Hammerhead_1 links to Rfam database...	0.33	0.29	0.40	4	936	7	0	6	1	10
RFA_00680	Hammerhead_1 links to Rfam database...	0.71	0.71	0.71	10	1114	7	0	4	3	4
RFA_00684	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	978	12	0	12	0	14
RFA_00685	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	979	11	0	11	0	14
RFA_00703	Hammerhead_1 links to Rfam database...	0.39	0.43	0.35	6	4261	24	3	8	13	8
RFA_00704	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	980	10	0	10	0	14
RFA_00705	Hammerhead_1 links to Rfam database...	0.74	0.71	0.77	10	1022	4	0	3	1	4
RFA_00706	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1026	9	1	8	0	14
RFA_00707	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1026	9	1	8	0	14
RFA_00708	Hammerhead_1 links to Rfam database...	0.35	0.29	0.44	4	1026	7	0	5	2	10
RFA_00709	Hammerhead_1 links to Rfam database...	0.23	0.21	0.27	3	979	9	0	8	1	11
RFA_00710	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	979	11	0	11	0	14
RFA_00711	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1026	9	0	9	0	14
RFA_00715	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	933	13	0	13	0	14
RFA_00716	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	936	10	2	8	0	14
RFA_00717	Hammerhead_1 links to Rfam database...	0.48	0.43	0.55	6	892	5	0	5	0	8
RFA_00730	s2m links to Rfam database...	0.28	0.25	0.33	3	894	6	1	5	0	9
RFA_00731	s2m links to Rfam database...	0.41	0.42	0.42	5	891	8	2	5	1	7
RFA_00733	s2m links to Rfam database...	0.43	0.42	0.45	5	892	7	2	4	1	7
RFA_00734	s2m links to Rfam database...	0.16	0.17	0.18	2	892	10	0	9	1	10
RFA_00736	s2m links to Rfam database...	0.41	0.42	0.42	5	891	8	2	5	1	7
RFA_00737	s2m links to Rfam database...	0.60	0.58	0.64	7	892	5	0	4	1	5
RFA_00745	s2m links to Rfam database...	0.43	0.42	0.45	5	935	7	2	4	1	7
RFA_00749	s2m links to Rfam database...	0.41	0.42	0.42	5	891	8	2	5	1	7
RFA_00758	s2m links to Rfam database...	-0.01	0.00	0.00	0	893	10	0	10	0	12
RFA_00762	s2m links to Rfam database...	0.39	0.42	0.38	5	890	8	2	6	0	7
RFA_00763	s2m links to Rfam database...	0.41	0.42	0.42	5	891	7	2	5	0	7
RFA_00764	s2m links to Rfam database...	0.43	0.42	0.45	5	892	7	2	4	1	7
RFA_00765	s2m links to Rfam database...	0.60	0.58	0.64	7	892	5	0	4	1	5
RFA_00767	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	4	0	0	4	0
RFA_00768	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	3	0	0	3	0
RFA_00769	Corona_pk3 links to Rfam database...	0.54	0.56	0.53	10	1934	9	4	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.97	0.94	1.00	17	1999	3	0	0	3	1
RFA_00773	Corona_pk3 links to Rfam database...	0.97	1.00	0.95	18	1934	4	1	0	3	0
RFA_00779	Corona_pk3 links to Rfam database...	0.83	0.83	0.83	15	1935	4	1	2	1	3
RFA_00808	RydC links to Rfam database...	1.00	1.00	1.00	16	2000	0	0	0	0	0
RFA_00809	RydC links to Rfam database...	0.79	0.81	0.76	13	2128	4	0	4	0	3

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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 RNASampler(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for RNASampler(seed)

2. Individual counts for RNASampler(seed) [ download as .csv ]

Performance of Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

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