CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

Overview

Metric	RNASampler(seed)		Cylofold
MCC	0.514	>	0.503
Average MCC ± 95% Confidence Intervals	0.393 ± 0.076	<	0.461 ± 0.083
Sensitivity	0.335	<	0.455
Positive Predictive Value	0.797	>	0.565
Total TP	412	<	560
Total TN	136155	>	135681
Total FP	125	<	507
Total FP CONTRA	30	<	53
Total FP INCONS	75	<	378
Total FP COMP	20	<	76
Total FN	818	>	670
P-value	1.80472700427e-05

^top

Performance plots

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

^top

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

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

Total Base Pair Counts
Total TP	412
Total TN	136155
Total FP	125
Total FP CONTRA	30
Total FP INCONS	75
Total FP COMP	20
Total FN	818

Total Scores
MCC	0.514
Average MCC ± 95% Confidence Intervals	0.393 ± 0.076
Sensitivity	0.335
Positive Predictive Value	0.797
Nr of predictions	75

^top

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_00213	Gammaretro_CES links to Rfam database...	0.76	0.59	1.00	24	5026	0	0	0	0	17
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_00695	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	7021	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_00781	Gammaretro_CES links to Rfam database...	0.85	0.72	1.00	23	5027	0	0	0	0	9
RFA_00786	Gammaretro_CES links to Rfam database...	0.79	0.63	1.00	20	5030	0	0	0	0	12
RFA_00791	Gammaretro_CES links to Rfam database...	0.71	0.56	0.90	18	5131	2	0	2	0	14
RFA_00792	Gammaretro_CES links to Rfam database...	0.81	0.72	0.92	23	5025	2	0	2	0	9
RFA_00801	Gammaretro_CES links to Rfam database...	0.74	0.63	0.87	20	5027	4	0	3	1	12
RFA_00809	RydC links to Rfam database...	0.36	0.38	0.35	6	2128	11	1	10	0	10

^top

Performance of Cylofold - scored lower in this pairwise comparison

1. Total counts & total scores for Cylofold

Total Base Pair Counts
Total TP	560
Total TN	135681
Total FP	507
Total FP CONTRA	53
Total FP INCONS	378
Total FP COMP	76
Total FN	670

Total Scores
MCC	0.503
Average MCC ± 95% Confidence Intervals	0.461 ± 0.083
Sensitivity	0.455
Positive Predictive Value	0.565
Nr of predictions	75

^top

2. Individual counts for Cylofold [ 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...	0.78	0.79	0.79	11	932	3	0	3	0	3
PDB_00012	mir-TAR links to Rfam database...	1.00	1.00	1.00	7	399	3	0	0	3	0
PDB_00213	Gammaretro_CES links to Rfam database...	0.66	0.61	0.71	25	5015	10	0	10	0	16
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...	0.68	0.70	0.67	16	2677	9	0	8	1	7
PDB_00810	s2m links to Rfam database...	0.51	0.41	0.64	7	1070	4	2	2	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...	0.79	0.69	0.90	9	893	2	0	1	1	4
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...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00416	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	3	0	0	3	0
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	8	0	0	8	0
RFA_00632	HDV_ribozyme links to Rfam database...	0.54	0.54	0.56	15	4068	12	2	10	0	13
RFA_00636	HDV_ribozyme links to Rfam database...	0.78	0.82	0.74	23	3974	8	7	1	0	5
RFA_00642	Vimentin3 links to Rfam database...	0.18	0.17	0.21	3	2912	11	1	10	0	15
RFA_00643	Vimentin3 links to Rfam database...	0.23	0.22	0.25	4	2195	12	1	11	0	14
RFA_00644	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2684	17	3	14	0	18
RFA_00645	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2397	18	4	14	0	18
RFA_00649	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2137	8	0	8	0	18
RFA_00651	Vimentin3 links to Rfam database...	0.30	0.28	0.33	5	2065	10	5	5	0	13
RFA_00653	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2130	15	3	12	0	18
RFA_00654	Vimentin3 links to Rfam database...	0.26	0.22	0.31	4	2402	10	1	8	1	14
RFA_00658	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1121	5	0	3	2	10
RFA_00659	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1118	12	0	10	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	981	10	1	8	1	14
RFA_00668	Hammerhead_1 links to Rfam database...	0.50	0.43	0.60	6	980	4	0	4	0	8
RFA_00672	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	895	9	0	8	1	13
RFA_00673	Hammerhead_1 links to Rfam database...	0.47	0.36	0.63	5	1120	4	0	3	1	9
RFA_00674	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1117	11	0	11	0	14
RFA_00675	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	981	9	1	8	0	14
RFA_00677	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	5	0	3	2	5
RFA_00678	Hammerhead_1 links to Rfam database...	0.53	0.29	1.00	4	942	0	0	0	0	10
RFA_00680	Hammerhead_1 links to Rfam database...	0.74	0.71	0.77	10	1115	6	0	3	3	4
RFA_00684	Hammerhead_1 links to Rfam database...	0.84	0.71	1.00	10	980	1	0	0	1	4
RFA_00685	Hammerhead_1 links to Rfam database...	0.47	0.36	0.63	5	982	3	0	3	0	9
RFA_00695	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	7010	23	4	7	12	14
RFA_00703	Hammerhead_1 links to Rfam database...	0.30	0.36	0.25	5	4258	19	4	11	4	9
RFA_00704	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	983	8	0	7	1	14
RFA_00705	Hammerhead_1 links to Rfam database...	0.84	0.71	1.00	10	1025	0	0	0	0	4
RFA_00706	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1026	9	0	9	0	14
RFA_00707	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1030	5	0	5	0	14
RFA_00708	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1028	3	0	3	0	10
RFA_00709	Hammerhead_1 links to Rfam database...	0.28	0.21	0.38	3	982	6	0	5	1	11
RFA_00710	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	981	9	0	9	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	939	7	0	7	0	14
RFA_00716	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	939	7	0	7	0	14
RFA_00717	Hammerhead_1 links to Rfam database...	0.35	0.29	0.44	4	894	5	0	5	0	10
RFA_00730	s2m links to Rfam database...	0.51	0.42	0.63	5	895	4	1	2	1	7
RFA_00731	s2m links to Rfam database...	0.48	0.42	0.56	5	894	5	1	3	1	7
RFA_00733	s2m links to Rfam database...	0.51	0.42	0.63	5	895	4	0	3	1	7
RFA_00734	s2m links to Rfam database...	0.18	0.17	0.22	2	894	8	0	7	1	10
RFA_00736	s2m links to Rfam database...	0.48	0.42	0.56	5	894	5	1	3	1	7
RFA_00737	s2m links to Rfam database...	0.43	0.42	0.45	5	892	7	0	6	1	7
RFA_00745	s2m links to Rfam database...	-0.01	0.00	0.00	0	938	8	1	7	0	12
RFA_00749	s2m links to Rfam database...	0.48	0.42	0.56	5	894	5	1	3	1	7
RFA_00758	s2m links to Rfam database...	-0.01	0.00	0.00	0	898	5	0	5	0	12
RFA_00762	s2m links to Rfam database...	0.31	0.33	0.31	4	890	9	2	7	0	8
RFA_00763	s2m links to Rfam database...	0.43	0.42	0.45	5	892	7	0	6	1	7
RFA_00764	s2m links to Rfam database...	0.51	0.42	0.63	5	895	4	0	3	1	7
RFA_00765	s2m links to Rfam database...	0.51	0.42	0.63	5	895	4	0	3	1	7
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	0	0	0	0	0
RFA_00769	Corona_pk3 links to Rfam database...	0.97	1.00	0.95	18	1934	1	1	0	0	0
RFA_00770	Corona_pk3 links to Rfam database...	0.88	0.78	1.00	14	2002	3	0	0	3	4
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...	0.97	0.94	1.00	17	1936	0	0	0	0	1
RFA_00781	Gammaretro_CES links to Rfam database...	0.64	0.66	0.64	21	5017	12	2	10	0	11
RFA_00786	Gammaretro_CES links to Rfam database...	0.33	0.31	0.36	10	5022	18	1	17	0	22
RFA_00791	Gammaretro_CES links to Rfam database...	0.51	0.44	0.61	14	5128	9	0	9	0	18
RFA_00792	Gammaretro_CES links to Rfam database...	0.78	0.72	0.85	23	5023	4	2	2	0	9
RFA_00801	Gammaretro_CES links to Rfam database...	0.82	0.75	0.89	24	5023	4	0	3	1	8
RFA_00809	RydC links to Rfam database...	0.79	0.81	0.76	13	2128	4	0	4	0	3

^top

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 Cylofold - scored lower in this pairwise comparison

1. Total counts & total scores for Cylofold

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