CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CMfinder(seed)		Sfold
MCC	0.571	>	0.545
Average MCC ± 95% Confidence Intervals	0.537 ± 0.067	>	0.502 ± 0.076
Sensitivity	0.439	<	0.497
Positive Predictive Value	0.747	>	0.604
Total TP	656	<	742
Total TN	258182	>	257832
Total FP	269	<	592
Total FP CONTRA	10	<	61
Total FP INCONS	212	<	425
Total FP COMP	47	<	106
Total FN	838	>	752
P-value	5.62644058675e-08

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Performance plots

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

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

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP	742
Total TN	257832
Total FP	592
Total FP CONTRA	61
Total FP INCONS	425
Total FP COMP	106
Total FN	752

Total Scores
MCC	0.545
Average MCC ± 95% Confidence Intervals	0.502 ± 0.076
Sensitivity	0.497
Positive Predictive Value	0.604
Nr of predictions	78

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2. Individual counts for Sfold [ 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...	-0.01	0.00	0.00	0	2678	24	1	22	1	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...	0.96	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...	0.76	0.63	0.92	33	10117	5	0	3	2	19
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...	0.66	0.69	0.63	24	13492	17	4	10	3	11
RFA_00604	Telomerase-cil links to Rfam database...	0.71	0.74	0.68	26	13492	24	2	10	12	9
RFA_00605	Telomerase-cil links to Rfam database...	0.39	0.34	0.44	12	15198	24	3	12	9	23
RFA_00607	Telomerase-cil links to Rfam database...	0.91	0.83	1.00	30	17736	7	0	0	7	6
RFA_00609	Telomerase-cil links to Rfam database...	0.78	0.78	0.78	29	17918	18	2	6	10	8
RFA_00610	Telomerase-cil links to Rfam database...	0.89	0.84	0.94	31	17172	15	0	2	13	6
RFA_00611	Telomerase-cil links to Rfam database...	0.81	0.71	0.93	25	13014	5	0	2	3	10
RFA_00613	Telomerase-cil links to Rfam database...	0.49	0.49	0.50	17	12846	19	7	10	2	18
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...	0.24	0.25	0.25	7	4067	21	2	19	0	21
RFA_00636	HDV_ribozyme links to Rfam database...	0.40	0.39	0.41	11	3978	16	2	14	0	17
RFA_00642	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	18
RFA_00643	Vimentin3 links to Rfam database...	0.24	0.22	0.27	4	2196	12	2	9	1	14
RFA_00644	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2689	12	0	12	0	18
RFA_00645	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2404	11	3	8	0	18
RFA_00649	Vimentin3 links to Rfam database...	0.37	0.33	0.43	6	2131	10	0	8	2	12
RFA_00651	Vimentin3 links to Rfam database...	0.14	0.11	0.18	2	2069	9	1	8	0	16
RFA_00653	Vimentin3 links to Rfam database...	0.34	0.33	0.35	6	2128	11	3	8	0	12
RFA_00654	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2401	14	2	12	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	1122	8	0	6	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...	0.22	0.21	0.25	3	978	10	1	8	1	11
RFA_00668	Hammerhead_1 links to Rfam database...	0.41	0.43	0.40	6	975	9	0	9	0	8
RFA_00672	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	896	7	0	7	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...	0.66	0.64	0.69	9	1115	5	0	4	1	5
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...	0.59	0.57	0.62	8	977	6	0	5	1	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...	0.59	0.57	0.62	8	977	6	0	5	1	6
RFA_00685	Hammerhead_1 links to Rfam database...	0.47	0.36	0.63	5	982	4	0	3	1	9
RFA_00704	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	981	9	0	9	0	14
RFA_00705	Hammerhead_1 links to Rfam database...	0.77	0.71	0.83	10	1023	2	0	2	0	4
RFA_00706	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1030	5	0	5	0	14
RFA_00707	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1028	7	1	6	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	980	10	0	10	0	14
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...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00715	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	937	9	0	9	0	14
RFA_00716	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	935	11	0	11	0	14
RFA_00717	Hammerhead_1 links to Rfam database...	0.72	0.64	0.82	9	892	2	0	2	0	5
RFA_00730	s2m links to Rfam database...	0.69	0.67	0.73	8	892	4	1	2	1	4
RFA_00731	s2m links to Rfam database...	0.66	0.67	0.67	8	891	5	1	3	1	4
RFA_00733	s2m links to Rfam database...	0.66	0.67	0.67	8	891	5	1	3	1	4
RFA_00734	s2m links to Rfam database...	0.61	0.67	0.57	8	889	7	1	5	1	4
RFA_00736	s2m links to Rfam database...	0.66	0.67	0.67	8	891	5	1	3	1	4
RFA_00737	s2m links to Rfam database...	0.96	0.92	1.00	11	892	1	0	0	1	1
RFA_00745	s2m links to Rfam database...	0.91	0.83	1.00	10	936	1	0	0	1	2
RFA_00749	s2m links to Rfam database...	0.66	0.67	0.67	8	891	5	1	3	1	4
RFA_00758	s2m links to Rfam database...	0.76	0.58	1.00	7	896	0	0	0	0	5
RFA_00762	s2m links to Rfam database...	0.64	0.67	0.62	8	890	5	1	4	0	4
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...	0.66	0.67	0.67	8	891	5	1	3	1	4
RFA_00765	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00769	Corona_pk3 links to Rfam database...	0.52	0.56	0.50	10	1933	10	4	6	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...	0.57	0.56	0.59	10	1936	7	1	6	0	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...	0.59	0.59	0.59	19	5018	13	2	11	0	13
RFA_00786	Gammaretro_CES links to Rfam database...	0.27	0.22	0.33	7	5029	14	1	13	0	25
RFA_00791	Gammaretro_CES links to Rfam database...	0.58	0.50	0.67	16	5127	8	1	7	0	16
RFA_00792	Gammaretro_CES links to Rfam database...	0.95	0.94	0.97	30	5019	2	0	1	1	2
RFA_00801	Gammaretro_CES links to Rfam database...	0.79	0.75	0.83	24	5021	6	0	5	1	8
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	2000	19	2	14	3	16
RFA_00809	RydC links to Rfam database...	0.37	0.38	0.38	6	2129	10	1	9	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 CMfinder(seed) - scored higher in this pairwise comparison

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

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

Performance of Sfold - scored lower in this pairwise comparison

1. Total counts & total scores for Sfold

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