CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Murlet(seed)		MCFold
MCC	0.431	>	0.427
Average MCC ± 95% Confidence Intervals	0.329 ± 0.087	<	0.460 ± 0.071
Sensitivity	0.236	<	0.470
Positive Predictive Value	0.793	>	0.396
Total TP	322	<	642
Total TN	200597	>	199381
Total FP	88	<	1237
Total FP CONTRA	0	<	150
Total FP INCONS	84	<	830
Total FP COMP	4	<	257
Total FN	1043	>	723
P-value	0.221270004692

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	322
Total TN	200597
Total FP	88
Total FP CONTRA	0
Total FP INCONS	84
Total FP COMP	4
Total FN	1043

Total Scores
MCC	0.431
Average MCC ± 95% Confidence Intervals	0.329 ± 0.087
Sensitivity	0.236
Positive Predictive Value	0.793
Nr of predictions	78

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2. Individual counts for Murlet(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...	0.53	0.29	1.00	4	942	2	0	0	2	10
PDB_00012	mir-TAR links to Rfam database...	0.65	0.43	1.00	3	403	0	0	0	0	4
PDB_00553	mir-TAR links to Rfam database...	0.45	0.27	0.75	3	461	1	0	1	0	8
PDB_00716	HDV_ribozyme links to Rfam database...	0.23	0.13	0.43	3	2694	4	0	4	0	20
PDB_00810	s2m links to Rfam database...	0.63	0.53	0.75	9	1069	3	0	3	0	8
PDB_01050	UnaL2 links to Rfam database...	0.55	0.31	1.00	4	626	1	0	0	1	9
PDB_01051	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	13
PDB_01152	HIV_FS2 links to Rfam database...	0.76	0.64	0.90	9	551	1	0	1	0	5
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...	0.00	0.00	0.00	0	1485	0	0	0	0	15
RFA_00433	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	0	0	0	0	15
RFA_00587	Y_RNA links to Rfam database...	0.00	0.00	0.00	0	4851	0	0	0	0	15
RFA_00603	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	13530	0	0	0	0	35
RFA_00604	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	13530	0	0	0	0	35
RFA_00610	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	17205	0	0	0	0	37
RFA_00611	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	13041	0	0	0	0	35
RFA_00613	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	12880	0	0	0	0	35
RFA_00615	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	13366	0	0	0	0	35
RFA_00636	HDV_ribozyme links to Rfam database...	0.21	0.11	0.43	3	3998	4	0	4	0	25
RFA_00642	Vimentin3 links to Rfam database...	0.57	0.44	0.73	8	2915	3	0	3	0	10
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...	0.42	0.33	0.55	6	2690	5	0	5	0	12
RFA_00645	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2407	8	0	8	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...	0.42	0.33	0.55	6	2069	5	0	5	0	12
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...	0.57	0.44	0.73	8	2404	3	0	3	0	10
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...	0.00	0.00	0.00	0	990	0	0	0	0	14
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...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00685	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00704	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	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...	0.00	0.00	0.00	0	946	0	0	0	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...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00731	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00733	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00734	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00736	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00737	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00745	s2m links to Rfam database...	1.00	1.00	1.00	12	934	0	0	0	0	0
RFA_00749	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00758	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00762	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00763	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00764	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00765	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00767	Corona_pk3 links to Rfam database...	0.47	0.33	0.67	6	1882	3	0	3	0	12
RFA_00768	Corona_pk3 links to Rfam database...	0.41	0.28	0.63	5	1883	3	0	3	0	13
RFA_00769	Corona_pk3 links to Rfam database...	0.57	0.44	0.73	8	1942	3	0	3	0	10
RFA_00770	Corona_pk3 links to Rfam database...	0.57	0.44	0.73	8	2005	3	0	3	0	10
RFA_00773	Corona_pk3 links to Rfam database...	0.41	0.28	0.63	5	1945	3	0	3	0	13
RFA_00779	Corona_pk3 links to Rfam database...	0.47	0.33	0.67	6	1944	3	0	3	0	12
RFA_00786	Gammaretro_CES links to Rfam database...	0.83	0.75	0.92	24	5024	2	0	2	0	8
RFA_00808	RydC links to Rfam database...	0.75	0.56	1.00	9	2007	0	0	0	0	7
RFA_00809	RydC links to Rfam database...	0.50	0.38	0.67	6	2136	3	0	3	0	10
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.49	0.24	1.00	6	4180	0	0	0	0	19
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.35	0.12	1.00	5	6323	1	0	0	1	36
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.41	0.17	1.00	6	5247	0	0	0	0	30
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	6	3735	0	0	0	0	24

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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	642
Total TN	199381
Total FP	1237
Total FP CONTRA	150
Total FP INCONS	830
Total FP COMP	257
Total FN	723

Total Scores
MCC	0.427
Average MCC ± 95% Confidence Intervals	0.460 ± 0.071
Sensitivity	0.470
Positive Predictive Value	0.396
Nr of predictions	78

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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_00012	mir-TAR links to Rfam database...	1.00	1.00	1.00	7	399	4	0	0	4	0
PDB_00553	mir-TAR links to Rfam database...	1.00	1.00	1.00	11	454	1	0	0	1	0
PDB_00716	HDV_ribozyme links to Rfam database...	0.22	0.26	0.19	6	2670	25	5	20	0	17
PDB_00810	s2m links to Rfam database...	0.74	0.76	0.72	13	1063	7	0	5	2	4
PDB_01050	UnaL2 links to Rfam database...	1.00	1.00	1.00	13	617	3	0	0	3	0
PDB_01051	Telomerase-cil links to Rfam database...	1.00	1.00	1.00	13	890	5	0	0	5	0
PDB_01152	HIV_FS2 links to Rfam database...	1.00	1.00	1.00	14	547	1	0	0	1	0
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	8	0	0	8	0
RFA_00416	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	9	0	0	9	0
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	8	0	0	8	0
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	28	0	0	28	0
RFA_00603	Telomerase-cil links to Rfam database...	0.67	0.60	0.75	21	13502	11	4	3	4	14
RFA_00604	Telomerase-cil links to Rfam database...	0.97	0.97	0.97	34	13495	15	0	1	14	1
RFA_00610	Telomerase-cil links to Rfam database...	0.70	0.54	0.91	20	17183	8	0	2	6	17
RFA_00611	Telomerase-cil links to Rfam database...	0.51	0.49	0.53	17	13009	20	6	9	5	18
RFA_00613	Telomerase-cil links to Rfam database...	0.24	0.23	0.26	8	12849	26	2	21	3	27
RFA_00615	Telomerase-cil links to Rfam database...	0.16	0.14	0.19	5	13339	22	5	17	0	30
RFA_00636	HDV_ribozyme links to Rfam database...	0.36	0.39	0.34	11	3973	29	0	21	8	17
RFA_00642	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2894	32	7	25	0	18
RFA_00643	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2186	27	2	23	2	18
RFA_00644	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2670	33	7	24	2	18
RFA_00645	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2387	28	3	25	0	18
RFA_00649	Vimentin3 links to Rfam database...	0.28	0.33	0.24	6	2120	22	2	17	3	12
RFA_00651	Vimentin3 links to Rfam database...	0.25	0.28	0.24	5	2059	21	0	16	5	13
RFA_00653	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2115	30	4	26	0	18
RFA_00654	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2386	29	4	25	0	18
RFA_00658	Hammerhead_1 links to Rfam database...	0.62	0.64	0.60	9	1113	10	0	6	4	5
RFA_00659	Hammerhead_1 links to Rfam database...	0.31	0.36	0.28	5	1110	16	1	12	3	9
RFA_00664	Hammerhead_1 links to Rfam database...	-0.02	0.00	0.00	0	974	16	0	16	0	14
RFA_00667	Hammerhead_1 links to Rfam database...	0.35	0.43	0.30	6	970	15	1	13	1	8
RFA_00668	Hammerhead_1 links to Rfam database...	0.23	0.29	0.20	4	970	16	3	13	0	10
RFA_00672	Hammerhead_1 links to Rfam database...	0.69	0.77	0.63	10	887	9	0	6	3	3
RFA_00673	Hammerhead_1 links to Rfam database...	0.60	0.64	0.56	9	1112	12	0	7	5	5
RFA_00674	Hammerhead_1 links to Rfam database...	0.96	0.93	1.00	13	1115	7	0	0	7	1
RFA_00675	Hammerhead_1 links to Rfam database...	-0.02	0.00	0.00	0	974	18	0	16	2	14
RFA_00677	Hammerhead_1 links to Rfam database...	0.46	0.50	0.44	7	974	12	0	9	3	7
RFA_00678	Hammerhead_1 links to Rfam database...	0.69	0.71	0.67	10	931	8	0	5	3	4
RFA_00680	Hammerhead_1 links to Rfam database...	0.62	0.64	0.60	9	1113	11	0	6	5	5
RFA_00684	Hammerhead_1 links to Rfam database...	0.57	0.57	0.57	8	976	10	0	6	4	6
RFA_00685	Hammerhead_1 links to Rfam database...	0.64	0.64	0.64	9	976	10	0	5	5	5
RFA_00704	Hammerhead_1 links to Rfam database...	0.37	0.43	0.33	6	972	13	1	11	1	8
RFA_00705	Hammerhead_1 links to Rfam database...	0.35	0.43	0.30	6	1015	14	4	10	0	8
RFA_00706	Hammerhead_1 links to Rfam database...	-0.02	0.00	0.00	0	1016	19	5	14	0	14
RFA_00707	Hammerhead_1 links to Rfam database...	0.36	0.43	0.32	6	1016	13	5	8	0	8
RFA_00708	Hammerhead_1 links to Rfam database...	0.64	0.64	0.64	9	1021	10	0	5	5	5
RFA_00709	Hammerhead_1 links to Rfam database...	0.38	0.43	0.35	6	973	12	0	11	1	8
RFA_00710	Hammerhead_1 links to Rfam database...	0.41	0.43	0.40	6	975	13	0	9	4	8
RFA_00711	Hammerhead_1 links to Rfam database...	-0.02	0.00	0.00	0	1017	18	5	13	0	14
RFA_00715	Hammerhead_1 links to Rfam database...	-0.02	0.00	0.00	0	929	17	0	17	0	14
RFA_00716	Hammerhead_1 links to Rfam database...	0.05	0.07	0.06	1	928	17	0	17	0	13
RFA_00717	Hammerhead_1 links to Rfam database...	0.36	0.43	0.32	6	884	13	0	13	0	8
RFA_00730	s2m links to Rfam database...	0.33	0.42	0.28	5	885	14	5	8	1	7
RFA_00731	s2m links to Rfam database...	0.34	0.42	0.29	5	886	13	4	8	1	7
RFA_00733	s2m links to Rfam database...	0.72	0.75	0.69	9	890	10	0	4	6	3
RFA_00734	s2m links to Rfam database...	0.51	0.58	0.47	7	888	12	1	7	4	5
RFA_00736	s2m links to Rfam database...	0.34	0.42	0.29	5	886	13	4	8	1	7
RFA_00737	s2m links to Rfam database...	0.34	0.42	0.29	5	886	13	4	8	1	7
RFA_00745	s2m links to Rfam database...	0.72	0.75	0.69	9	933	11	0	4	7	3
RFA_00749	s2m links to Rfam database...	0.34	0.42	0.29	5	886	13	4	8	1	7
RFA_00758	s2m links to Rfam database...	0.59	0.67	0.53	8	888	10	2	5	3	4
RFA_00762	s2m links to Rfam database...	0.33	0.42	0.28	5	885	13	5	8	0	7
RFA_00763	s2m links to Rfam database...	0.72	0.75	0.69	9	890	10	0	4	6	3
RFA_00764	s2m links to Rfam database...	0.72	0.75	0.69	9	890	10	0	4	6	3
RFA_00765	s2m links to Rfam database...	0.72	0.75	0.69	9	890	10	0	4	6	3
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_00786	Gammaretro_CES links to Rfam database...	0.13	0.16	0.12	5	5008	37	5	32	0	27
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
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.69	0.80	0.61	20	4153	20	5	8	7	5
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.33	0.37	0.31	15	6280	35	2	31	2	26
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.61	0.67	0.56	24	5210	24	1	18	5	12
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.33	0.37	0.31	11	3705	27	2	23	2	19

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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 Murlet(seed) - scored higher in this pairwise comparison

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

2. Individual counts for Murlet(seed) [ 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 ]