CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Contrafold		CMfinder(seed)
MCC	0.594	>	0.571
Average MCC ± 95% Confidence Intervals	0.544 ± 0.076	>	0.537 ± 0.067
Sensitivity	0.546	>	0.439
Positive Predictive Value	0.650	<	0.747
Total TP	816	>	656
Total TN	257804	<	258182
Total FP	592	>	269
Total FP CONTRA	55	>	10
Total FP INCONS	385	>	212
Total FP COMP	152	>	47
Total FN	678	<	838
P-value	4.83792096436e-08

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Performance plots

Comparison of performance of Contrafold and CMfinder(seed). 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 Contrafold and CMfinder(seed)).
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 Contrafold and CMfinder(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Contrafold and CMfinder(seed). 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 Contrafold and CMfinder(seed)).

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Performance of Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP	816
Total TN	257804
Total FP	592
Total FP CONTRA	55
Total FP INCONS	385
Total FP COMP	152
Total FN	678

Total Scores
MCC	0.594
Average MCC ± 95% Confidence Intervals	0.544 ± 0.076
Sensitivity	0.546
Positive Predictive Value	0.650
Nr of predictions	78

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2. Individual counts for Contrafold [ 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...	0.94	0.88	1.00	36	5014	0	0	0	0	5
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...	0.33	0.30	0.37	7	2682	13	0	12	1	16
PDB_00810	s2m links to Rfam database...	0.77	0.71	0.86	12	1067	3	0	2	1	5
PDB_01050	UnaL2 links to Rfam database...	0.96	0.92	1.00	12	618	2	0	0	2	1
PDB_01051	Telomerase-cil links to Rfam database...	0.88	0.85	0.92	11	891	5	0	1	4	2
PDB_01092	glmS links to Rfam database...	0.70	0.65	0.76	34	10108	14	2	9	3	18
PDB_01152	HIV_FS2 links to Rfam database...	0.96	0.93	1.00	13	548	0	0	0	0	1
RFA_00603	Telomerase-cil links to Rfam database...	0.73	0.71	0.76	25	13497	8	4	4	0	10
RFA_00604	Telomerase-cil links to Rfam database...	0.71	0.74	0.68	26	13492	26	2	10	14	9
RFA_00605	Telomerase-cil links to Rfam database...	0.35	0.34	0.36	12	15192	35	2	19	14	23
RFA_00607	Telomerase-cil links to Rfam database...	0.87	0.81	0.94	29	17735	11	0	2	9	7
RFA_00609	Telomerase-cil links to Rfam database...	0.76	0.78	0.74	29	17916	27	2	8	17	8
RFA_00610	Telomerase-cil links to Rfam database...	0.90	0.86	0.94	32	17171	20	0	2	18	5
RFA_00611	Telomerase-cil links to Rfam database...	0.82	0.74	0.90	26	13012	6	0	3	3	9
RFA_00613	Telomerase-cil links to Rfam database...	0.60	0.51	0.69	18	12854	9	3	5	1	17
RFA_00615	Telomerase-cil links to Rfam database...	0.63	0.57	0.69	20	13337	9	4	5	0	15
RFA_00632	HDV_ribozyme links to Rfam database...	0.38	0.39	0.37	11	4065	19	0	19	0	17
RFA_00636	HDV_ribozyme links to Rfam database...	0.60	0.64	0.56	18	3973	14	4	10	0	10
RFA_00642	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2915	11	2	9	0	18
RFA_00643	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2202	9	1	8	0	18
RFA_00644	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2692	9	1	8	0	18
RFA_00645	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2402	13	3	10	0	18
RFA_00649	Vimentin3 links to Rfam database...	0.26	0.22	0.31	4	2132	9	6	3	0	14
RFA_00651	Vimentin3 links to Rfam database...	0.40	0.33	0.50	6	2068	6	1	5	0	12
RFA_00653	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2133	12	2	10	0	18
RFA_00654	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2400	15	2	13	0	18
RFA_00658	Hammerhead_1 links to Rfam database...	0.59	0.50	0.70	7	1118	5	0	3	2	7
RFA_00659	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1120	10	1	7	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...	0.29	0.29	0.31	4	977	10	1	8	1	10
RFA_00668	Hammerhead_1 links to Rfam database...	0.53	0.43	0.67	6	981	3	0	3	0	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...	0.42	0.36	0.50	5	1118	6	0	5	1	9
RFA_00674	Hammerhead_1 links to Rfam database...	0.96	0.93	1.00	13	1115	1	0	0	1	1
RFA_00675	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	980	11	0	10	1	14
RFA_00677	Hammerhead_1 links to Rfam database...	0.59	0.57	0.62	8	977	7	0	5	2	6
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...	0.66	0.64	0.69	9	977	5	0	4	1	5
RFA_00685	Hammerhead_1 links to Rfam database...	0.44	0.36	0.56	5	981	4	0	4	0	9
RFA_00704	Hammerhead_1 links to Rfam database...	0.32	0.21	0.50	3	984	5	0	3	2	11
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...	0.37	0.29	0.50	4	1027	4	0	4	0	10
RFA_00707	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1027	8	1	7	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...	-0.01	0.00	0.00	0	981	10	0	9	1	14
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	936	10	0	10	0	14
RFA_00716	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	937	9	0	9	0	14
RFA_00717	Hammerhead_1 links to Rfam database...	0.66	0.64	0.69	9	890	4	0	4	0	5
RFA_00730	s2m links to Rfam database...	0.75	0.75	0.75	9	891	5	0	3	2	3
RFA_00731	s2m links to Rfam database...	0.83	0.83	0.83	10	891	4	0	2	2	2
RFA_00733	s2m links to Rfam database...	0.83	0.83	0.83	10	891	4	0	2	2	2
RFA_00734	s2m links to Rfam database...	0.83	0.83	0.83	10	891	5	0	2	3	2
RFA_00736	s2m links to Rfam database...	0.83	0.83	0.83	10	891	4	0	2	2	2
RFA_00737	s2m links to Rfam database...	0.83	0.83	0.83	10	891	4	0	2	2	2
RFA_00745	s2m links to Rfam database...	0.66	0.67	0.67	8	934	6	1	3	2	4
RFA_00749	s2m links to Rfam database...	0.83	0.83	0.83	10	891	4	0	2	2	2
RFA_00758	s2m links to Rfam database...	0.60	0.58	0.64	7	892	5	1	3	1	5
RFA_00762	s2m links to Rfam database...	0.64	0.67	0.62	8	890	6	1	4	1	4
RFA_00763	s2m links to Rfam database...	0.83	0.83	0.83	10	891	4	0	2	2	2
RFA_00764	s2m links to Rfam database...	0.83	0.83	0.83	10	891	4	0	2	2	2
RFA_00765	s2m links to Rfam database...	0.83	0.83	0.83	10	891	4	0	2	2	2
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...	0.68	0.56	0.83	10	2004	5	0	2	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	4	1	0	3	8
RFA_00779	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	0	2	0	8
RFA_00781	Gammaretro_CES links to Rfam database...	0.98	0.97	1.00	31	5019	2	0	0	2	1
RFA_00786	Gammaretro_CES links to Rfam database...	0.48	0.44	0.54	14	5024	14	1	11	2	18
RFA_00791	Gammaretro_CES links to Rfam database...	0.89	0.88	0.90	28	5120	6	2	1	3	4
RFA_00792	Gammaretro_CES links to Rfam database...	0.95	0.94	0.97	30	5019	3	0	1	2	2
RFA_00801	Gammaretro_CES links to Rfam database...	0.81	0.78	0.83	25	5020	8	0	5	3	7
RFA_00808	RydC links to Rfam database...	0.68	0.56	0.82	9	2005	2	0	2	0	7
RFA_00809	RydC links to Rfam database...	0.40	0.38	0.43	6	2131	8	0	8	0	10

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Performance of CMfinder(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	656
Total TN	258182
Total FP	269
Total FP CONTRA	10
Total FP INCONS	212
Total FP COMP	47
Total FN	838

Total Scores
MCC	0.571
Average MCC ± 95% Confidence Intervals	0.537 ± 0.067
Sensitivity	0.439
Positive Predictive Value	0.747
Nr of predictions	78

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2. Individual counts for CMfinder(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...	0.47	0.36	0.63	5	938	3	0	3	0	9
PDB_00012	mir-TAR links to Rfam database...	1.00	1.00	1.00	7	399	2	0	0	2	0
PDB_00213	Gammaretro_CES links to Rfam database...	0.85	0.73	1.00	30	5020	0	0	0	0	11
PDB_00553	mir-TAR links to Rfam database...	0.00	0.00	0.00	0	465	0	0	0	0	11
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2688	13	0	13	0	23
PDB_00810	s2m links to Rfam database...	0.76	0.59	1.00	10	1071	0	0	0	0	7
PDB_01050	UnaL2 links to Rfam database...	0.68	0.46	1.00	6	624	1	0	0	1	7
PDB_01051	Telomerase-cil links to Rfam database...	0.83	0.69	1.00	9	894	4	0	0	4	4
PDB_01092	glmS links to Rfam database...	0.38	0.21	0.69	11	10137	6	0	5	1	41
PDB_01152	HIV_FS2 links to Rfam database...	0.92	0.86	1.00	12	549	0	0	0	0	2
RFA_00603	Telomerase-cil links to Rfam database...	0.70	0.60	0.81	21	13504	7	0	5	2	14
RFA_00604	Telomerase-cil links to Rfam database...	0.63	0.51	0.78	18	13507	8	0	5	3	17
RFA_00605	Telomerase-cil links to Rfam database...	0.14	0.06	0.33	2	15219	5	0	4	1	33
RFA_00607	Telomerase-cil links to Rfam database...	0.08	0.06	0.13	2	17750	15	3	11	1	34
RFA_00609	Telomerase-cil links to Rfam database...	0.32	0.22	0.47	8	17938	12	2	7	3	29
RFA_00610	Telomerase-cil links to Rfam database...	0.39	0.30	0.52	11	17184	13	2	8	3	26
RFA_00611	Telomerase-cil links to Rfam database...	0.65	0.51	0.82	18	13019	5	0	4	1	17
RFA_00613	Telomerase-cil links to Rfam database...	0.70	0.57	0.87	20	12857	4	0	3	1	15
RFA_00615	Telomerase-cil links to Rfam database...	0.57	0.49	0.68	17	13341	10	0	8	2	18
RFA_00632	HDV_ribozyme links to Rfam database...	0.27	0.25	0.29	7	4071	17	0	17	0	21
RFA_00636	HDV_ribozyme links to Rfam database...	0.71	0.64	0.78	18	3982	5	2	3	0	10
RFA_00642	Vimentin3 links to Rfam database...	0.44	0.28	0.71	5	2919	2	0	2	0	13
RFA_00643	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2203	8	0	8	0	18
RFA_00644	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2693	8	0	8	0	18
RFA_00645	Vimentin3 links to Rfam database...	0.29	0.17	0.50	3	2409	3	0	3	0	15
RFA_00649	Vimentin3 links to Rfam database...	0.35	0.22	0.57	4	2138	3	0	3	0	14
RFA_00651	Vimentin3 links to Rfam database...	0.35	0.22	0.57	4	2073	3	0	3	0	14
RFA_00653	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2137	8	0	8	0	18
RFA_00654	Vimentin3 links to Rfam database...	0.38	0.22	0.67	4	2409	2	0	2	0	14
RFA_00658	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1121	4	0	3	1	10
RFA_00659	Hammerhead_1 links to Rfam database...	0.23	0.14	0.40	2	1123	4	0	3	1	12
RFA_00664	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	983	4	0	3	1	10
RFA_00667	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	983	4	0	3	1	10
RFA_00668	Hammerhead_1 links to Rfam database...	0.35	0.21	0.60	3	985	3	0	2	1	11
RFA_00672	Hammerhead_1 links to Rfam database...	0.41	0.31	0.57	4	896	3	0	3	0	9
RFA_00673	Hammerhead_1 links to Rfam database...	0.23	0.14	0.40	2	1123	4	0	3	1	12
RFA_00674	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1121	4	0	3	1	10
RFA_00675	Hammerhead_1 links to Rfam database...	0.35	0.21	0.60	3	985	3	0	2	1	11
RFA_00677	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	983	4	0	3	1	10
RFA_00678	Hammerhead_1 links to Rfam database...	0.43	0.29	0.67	4	940	3	0	2	1	10
RFA_00680	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1121	4	0	3	1	10
RFA_00684	Hammerhead_1 links to Rfam database...	0.43	0.29	0.67	4	984	3	0	2	1	10
RFA_00685	Hammerhead_1 links to Rfam database...	0.32	0.21	0.50	3	984	4	0	3	1	11
RFA_00704	Hammerhead_1 links to Rfam database...	0.32	0.21	0.50	3	984	4	0	3	1	11
RFA_00705	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1028	4	0	3	1	10
RFA_00706	Hammerhead_1 links to Rfam database...	0.43	0.29	0.67	4	1029	3	0	2	1	10
RFA_00707	Hammerhead_1 links to Rfam database...	0.43	0.29	0.67	4	1029	3	0	2	1	10
RFA_00708	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1028	4	0	3	1	10
RFA_00709	Hammerhead_1 links to Rfam database...	0.32	0.21	0.50	3	984	4	0	3	1	11
RFA_00710	Hammerhead_1 links to Rfam database...	0.32	0.21	0.50	3	984	3	0	3	0	11
RFA_00711	Hammerhead_1 links to Rfam database...	0.43	0.29	0.67	4	1029	3	0	2	1	10
RFA_00715	Hammerhead_1 links to Rfam database...	0.30	0.14	0.67	2	943	2	0	1	1	12
RFA_00716	Hammerhead_1 links to Rfam database...	0.43	0.29	0.67	4	940	3	0	2	1	10
RFA_00717	Hammerhead_1 links to Rfam database...	0.30	0.21	0.43	3	896	4	0	4	0	11
RFA_00730	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00731	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00733	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00734	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00736	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00737	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00745	s2m links to Rfam database...	0.91	0.83	1.00	10	936	0	0	0	0	2
RFA_00749	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00758	s2m links to Rfam database...	0.86	0.75	1.00	9	894	0	0	0	0	3
RFA_00762	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00763	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00764	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00765	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00769	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	1944	0	0	0	0	9
RFA_00770	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	2007	0	0	0	0	9
RFA_00773	Corona_pk3 links to Rfam database...	0.00	0.00	0.00	0	1949	4	0	4	0	18
RFA_00779	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	1944	0	0	0	0	9
RFA_00781	Gammaretro_CES links to Rfam database...	0.97	0.94	1.00	30	5020	0	0	0	0	2
RFA_00786	Gammaretro_CES links to Rfam database...	0.95	0.91	1.00	29	5021	0	0	0	0	3
RFA_00791	Gammaretro_CES links to Rfam database...	0.92	0.88	0.97	28	5122	1	0	1	0	4
RFA_00792	Gammaretro_CES links to Rfam database...	0.97	0.94	1.00	30	5020	0	0	0	0	2
RFA_00801	Gammaretro_CES links to Rfam database...	0.95	0.91	1.00	29	5021	0	0	0	0	3
RFA_00808	RydC links to Rfam database...	0.68	0.56	0.82	9	2005	2	0	2	0	7
RFA_00809	RydC links to Rfam database...	0.41	0.38	0.46	6	2132	7	1	6	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 Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

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

Performance of CMfinder(seed) - scored lower in this pairwise comparison

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

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