CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAalifold(seed)		MCFold
MCC	0.612	>	0.476
Average MCC ± 95% Confidence Intervals	0.565 ± 0.045	>	0.511 ± 0.047
Sensitivity	0.404	<	0.525
Positive Predictive Value	0.932	>	0.438
Total TP	1569	<	2040
Total TN	609640	>	606663
Total FP	167	<	3544
Total FP CONTRA	15	<	369
Total FP INCONS	100	<	2252
Total FP COMP	52	<	923
Total FN	2318	>	1847
P-value	3.56938820447e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	1569
Total TN	609640
Total FP	167
Total FP CONTRA	15
Total FP INCONS	100
Total FP COMP	52
Total FN	2318

Total Scores
MCC	0.612
Average MCC ± 95% Confidence Intervals	0.565 ± 0.045
Sensitivity	0.404
Positive Predictive Value	0.932
Nr of predictions	175

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2. Individual counts for RNAalifold(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...	0.59	0.36	1.00	5	941	0	0	0	0	9
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...	0.52	0.27	1.00	3	462	0	0	0	0	8
PDB_00716	HDV_ribozyme links to Rfam database...	0.60	0.43	0.83	10	2689	2	0	2	0	13
PDB_00741	Entero_5_CRE links to Rfam database...	0.68	0.47	1.00	8	695	0	0	0	0	9
PDB_00810	s2m links to Rfam database...	0.84	0.71	1.00	12	1069	0	0	0	0	5
PDB_00828	Purine links to Rfam database...	0.70	0.59	0.84	16	2466	3	2	1	0	11
PDB_00829	Purine links to Rfam database...	0.75	0.67	0.84	16	2259	3	2	1	0	8
PDB_00876	HIV_FE links to Rfam database...	0.59	0.40	0.89	8	981	1	0	1	0	12
PDB_01020	Purine links to Rfam database...	0.73	0.65	0.83	15	2260	4	2	1	1	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...	0.96	0.92	1.00	12	891	4	0	0	4	1
PDB_01073	SAM links to Rfam database...	0.80	0.65	1.00	22	4349	1	0	0	1	12
PDB_01114	TPP links to Rfam database...	0.77	0.59	1.00	16	2834	0	0	0	0	11
PDB_01152	HIV_FS2 links to Rfam database...	0.80	0.71	0.91	10	550	1	0	1	0	4
RFA_00389	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	1	0	0	1	2
RFA_00390	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	1	0	0	1	2
RFA_00391	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	1	0	0	1	2
RFA_00396	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	1	0	0	1	2
RFA_00402	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	1	0	0	1	2
RFA_00409	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	1	0	0	1	2
RFA_00416	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1472	1	0	0	1	2
RFA_00425	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1640	1	0	0	1	2
RFA_00427	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1472	1	0	0	1	2
RFA_00433	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	1	0	0	1	2
RFA_00434	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	1	0	0	1	2
RFA_00436	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	1	0	0	1	2
RFA_00440	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1472	1	0	0	1	2
RFA_00442	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	1	0	0	1	2
RFA_00444	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1527	1	0	0	1	2
RFA_00446	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1472	1	0	0	1	2
RFA_00449	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1472	1	0	0	1	2
RFA_00582	Y_RNA links to Rfam database...	0.68	0.47	1.00	7	5988	0	0	0	0	8
RFA_00583	Y_RNA links to Rfam database...	0.68	0.47	1.00	7	4943	0	0	0	0	8
RFA_00584	Y_RNA links to Rfam database...	0.68	0.47	1.00	7	2919	0	0	0	0	8
RFA_00585	Y_RNA links to Rfam database...	0.68	0.47	1.00	7	4844	0	0	0	0	8
RFA_00586	Y_RNA links to Rfam database...	0.68	0.47	1.00	7	3909	0	0	0	0	8
RFA_00587	Y_RNA links to Rfam database...	0.68	0.47	1.00	7	4844	0	0	0	0	8
RFA_00588	Y_RNA links to Rfam database...	0.68	0.47	1.00	7	4553	0	0	0	0	8
RFA_00589	Y_RNA links to Rfam database...	0.63	0.40	1.00	6	4365	0	0	0	0	9
RFA_00594	Y_RNA links to Rfam database...	0.68	0.47	1.00	7	2768	0	0	0	0	8
RFA_00596	Y_RNA links to Rfam database...	0.58	0.33	1.00	5	5990	0	0	0	0	10
RFA_00603	Telomerase-cil links to Rfam database...	0.94	0.89	1.00	31	13499	0	0	0	0	4
RFA_00604	Telomerase-cil links to Rfam database...	0.94	0.89	1.00	31	13499	0	0	0	0	4
RFA_00610	Telomerase-cil links to Rfam database...	0.92	0.84	1.00	31	17174	0	0	0	0	6
RFA_00611	Telomerase-cil links to Rfam database...	0.94	0.89	1.00	31	13010	0	0	0	0	4
RFA_00613	Telomerase-cil links to Rfam database...	0.94	0.89	1.00	31	12849	0	0	0	0	4
RFA_00615	Telomerase-cil links to Rfam database...	0.83	0.77	0.90	27	13336	3	0	3	0	8
RFA_00636	HDV_ribozyme links to Rfam database...	0.49	0.32	0.75	9	3993	3	2	1	0	19
RFA_00642	Vimentin3 links to Rfam database...	0.54	0.44	0.67	8	2914	4	0	4	0	10
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...	0.44	0.33	0.60	6	2691	4	0	4	0	12
RFA_00645	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2406	9	1	8	0	18
RFA_00649	Vimentin3 links to Rfam database...	0.44	0.33	0.60	6	2135	4	0	4	0	12
RFA_00651	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2071	9	1	8	0	18
RFA_00653	Vimentin3 links to Rfam database...	0.42	0.33	0.55	6	2134	5	0	5	0	12
RFA_00654	Vimentin3 links to Rfam database...	0.52	0.44	0.62	8	2402	5	0	5	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...	0.65	0.56	0.77	10	1878	3	0	3	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1878	3	0	3	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1940	3	0	3	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	2003	3	0	3	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1940	3	0	3	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1940	3	0	3	0	8
RFA_00786	Gammaretro_CES links to Rfam database...	0.68	0.63	0.74	20	5023	7	1	6	0	12
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_00001	Bacteria_large_SRP links to Rfam database...	0.81	0.65	1.00	26	6760	1	0	0	1	14
SRP_00038	Bacteria_small_SRP links to Rfam database...	0.49	0.24	1.00	8	5042	1	0	0	1	25
SRP_00040	Bacteria_small_SRP links to Rfam database...	0.51	0.26	1.00	8	5557	1	0	0	1	23
SRP_00042	Bacteria_small_SRP links to Rfam database...	0.56	0.32	1.00	8	3997	1	0	0	1	17
SRP_00043	Bacteria_small_SRP links to Rfam database...	0.56	0.31	1.00	9	5041	0	0	0	0	20
SRP_00044	Bacteria_small_SRP links to Rfam database...	0.53	0.28	1.00	9	6096	0	0	0	0	23
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.53	0.28	1.00	9	4744	0	0	0	0	23
SRP_00051	Bacteria_small_SRP links to Rfam database...	0.52	0.27	1.00	8	5452	1	0	0	1	22
SRP_00054	Bacteria_small_SRP links to Rfam database...	0.50	0.25	1.00	8	5557	1	0	0	1	24
SRP_00057	Bacteria_small_SRP links to Rfam database...	0.51	0.26	1.00	9	6319	0	0	0	0	26
SRP_00072	Bacteria_small_SRP links to Rfam database...	0.52	0.28	1.00	8	6320	1	0	0	1	21
SRP_00074	Bacteria_small_SRP links to Rfam database...	0.52	0.28	1.00	8	6547	1	0	0	1	21
SRP_00094	Bacteria_small_SRP links to Rfam database...	0.61	0.38	1.00	9	4086	0	0	0	0	15
SRP_00095	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	9	3996	0	0	0	0	16
SRP_00098	Bacteria_small_SRP links to Rfam database...	0.49	0.24	1.00	9	6432	0	0	0	0	28
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.51	0.26	1.00	9	5556	0	0	0	0	25
SRP_00106	Bacteria_large_SRP links to Rfam database...	0.70	0.72	0.69	18	5227	10	3	5	2	7
SRP_00107	Bacteria_small_SRP links to Rfam database...	0.65	0.42	1.00	8	3647	1	0	0	1	11
SRP_00121	Bacteria_small_SRP links to Rfam database...	0.56	0.32	1.00	8	4270	1	0	0	1	17
SRP_00128	Bacteria_small_SRP links to Rfam database...	0.50	0.25	1.00	9	6777	0	0	0	0	27
SRP_00132	Bacteria_small_SRP links to Rfam database...	0.56	0.31	1.00	9	4842	0	0	0	0	20
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.70	0.62	0.78	18	5972	9	0	5	4	11
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	9	4177	0	0	0	0	16
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.44	0.20	1.00	8	6320	1	0	0	1	33
SRP_00145	Bacteria_small_SRP links to Rfam database...	0.47	0.23	1.00	9	6319	0	0	0	0	31
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.50	0.25	1.00	9	5244	0	0	0	0	27
SRP_00161	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	8	2842	1	0	0	1	14
SRP_00162	Bacteria_small_SRP links to Rfam database...	0.62	0.39	1.00	9	2917	0	0	0	0	14
SRP_00163	Bacteria_small_SRP links to Rfam database...	0.55	0.31	1.00	8	3478	1	0	0	1	18
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.56	0.32	1.00	8	4087	1	0	0	1	17
SRP_00194	Bacteria_small_SRP links to Rfam database...	0.38	0.24	0.63	5	3232	3	0	3	0	16
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.50	0.25	1.00	9	6894	0	0	0	0	27
SRP_00209	Bacteria_small_SRP links to Rfam database...	0.58	0.33	1.00	9	4647	0	0	0	0	18
SRP_00213	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	9	4177	0	0	0	0	16
SRP_00215	Bacteria_small_SRP links to Rfam database...	0.56	0.32	1.00	8	3232	0	0	0	0	17
SRP_00216	Bacteria_small_SRP links to Rfam database...	0.58	0.33	1.00	9	3394	0	0	0	0	18
SRP_00217	Bacteria_small_SRP links to Rfam database...	0.61	0.38	1.00	9	3312	0	0	0	0	15
SRP_00219	Bacteria_small_SRP links to Rfam database...	0.59	0.35	1.00	8	3313	1	0	0	1	15
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.51	0.26	1.00	9	5451	0	0	0	0	25
SRP_00233	Bacteria_small_SRP links to Rfam database...	0.52	0.27	1.00	9	5142	0	0	0	0	24
SRP_00243	Bacteria_small_SRP links to Rfam database...	0.54	0.29	1.00	9	5142	0	0	0	0	22
SRP_00244	Bacteria_small_SRP links to Rfam database...	0.45	0.21	1.00	8	6895	1	0	0	1	31
SRP_00250	Bacteria_small_SRP links to Rfam database...	0.50	0.25	1.00	9	6777	0	0	0	0	27
SRP_00251	Bacteria_small_SRP links to Rfam database...	0.50	0.25	1.00	9	7012	0	0	0	0	27
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.49	0.28	0.89	8	4647	1	0	1	0	21
SRP_00269	Bacteria_small_SRP links to Rfam database...	0.52	0.27	1.00	9	5041	0	0	0	0	24
SRP_00271	Bacteria_small_SRP links to Rfam database...	0.61	0.38	1.00	9	3231	0	0	0	0	15
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.47	0.23	1.00	9	6777	0	0	0	0	31
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.49	0.24	1.00	9	6894	0	0	0	0	29
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.55	0.30	1.00	9	3732	0	0	0	0	21
SRP_00295	Bacteria_small_SRP links to Rfam database...	0.46	0.21	1.00	8	6895	1	0	0	1	30
SRP_00303	Bacteria_small_SRP links to Rfam database...	0.53	0.28	1.00	9	6661	0	0	0	0	23
SRP_00310	Bacteria_small_SRP links to Rfam database...	0.62	0.39	1.00	9	2917	0	0	0	0	14
SRP_00312	Bacteria_small_SRP links to Rfam database...	0.54	0.30	1.00	8	4178	1	0	0	1	19
SRP_00315	Bacteria_small_SRP links to Rfam database...	0.62	0.39	1.00	9	2917	0	0	0	0	14
SRP_00318	Bacteria_small_SRP links to Rfam database...	0.62	0.39	1.00	9	2994	0	0	0	0	14
SRP_00324	Bacteria_small_SRP links to Rfam database...	0.49	0.28	0.89	8	5347	1	0	1	0	21
SRP_00325	Bacteria_small_SRP links to Rfam database...	0.52	0.27	1.00	9	4362	0	0	0	0	24
SRP_00326	Bacteria_small_SRP links to Rfam database...	0.51	0.26	1.00	8	5042	1	0	0	1	23
SRP_00333	Bacteria_small_SRP links to Rfam database...	0.51	0.26	1.00	9	5142	0	0	0	0	25
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.51	0.26	1.00	8	4745	1	0	0	1	23
SRP_00342	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	9	3996	0	0	0	0	16
SRP_00350	Bacteria_small_SRP links to Rfam database...	0.58	0.33	1.00	9	3907	0	0	0	0	18
SRP_00356	Bacteria_small_SRP links to Rfam database...	0.52	0.27	1.00	8	5042	1	0	0	1	22
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.50	0.25	1.00	9	5347	0	0	0	0	27
SRP_00358	Bacteria_small_SRP links to Rfam database...	0.51	0.26	1.00	9	6319	0	0	0	0	26
SRP_00363	Bacteria_small_SRP links to Rfam database...	0.55	0.30	1.00	9	4744	0	0	0	0	21
SRP_00365	Bacteria_small_SRP links to Rfam database...	0.51	0.30	0.89	8	3394	1	0	1	0	19
SRP_00367	Bacteria_small_SRP links to Rfam database...	0.51	0.26	1.00	9	6777	0	0	0	0	26
SRP_00369	Bacteria_small_SRP links to Rfam database...	0.51	0.26	1.00	9	5769	0	0	0	0	26
SRP_00383	Bacteria_small_SRP links to Rfam database...	0.58	0.33	1.00	8	3232	1	0	0	1	16

^top

Performance of MCFold - scored lower in this pairwise comparison

1. Total counts & total scores for MCFold

Total Base Pair Counts
Total TP	2040
Total TN	606663
Total FP	3544
Total FP CONTRA	369
Total FP INCONS	2252
Total FP COMP	923
Total FN	1847

Total Scores
MCC	0.476
Average MCC ± 95% Confidence Intervals	0.511 ± 0.047
Sensitivity	0.525
Positive Predictive Value	0.438
Nr of predictions	175

^top

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_00741	Entero_5_CRE links to Rfam database...	1.00	1.00	1.00	17	686	0	0	0	0	0
PDB_00810	s2m links to Rfam database...	0.74	0.76	0.72	13	1063	7	0	5	2	4
PDB_00828	Purine links to Rfam database...	0.34	0.37	0.33	10	2455	22	1	19	2	17
PDB_00829	Purine links to Rfam database...	0.25	0.29	0.23	7	2248	23	6	17	0	17
PDB_00876	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
PDB_01020	Purine links to Rfam database...	0.29	0.30	0.29	7	2254	20	2	15	3	16
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_01073	SAM links to Rfam database...	0.52	0.56	0.49	19	4332	22	1	19	2	15
PDB_01114	TPP links to Rfam database...	0.54	0.59	0.50	16	2818	18	1	15	2	11
PDB_01152	HIV_FS2 links to Rfam database...	1.00	1.00	1.00	14	547	1	0	0	1	0
RFA_00389	Hammerhead_3 links to Rfam database...	0.87	0.87	0.87	13	1416	9	0	2	7	2
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	8	0	0	8	0
RFA_00391	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	8	0	0	8	0
RFA_00396	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	8	0	0	8	0
RFA_00402	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	8	0	0	8	0
RFA_00409	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_00425	Hammerhead_3 links to Rfam database...	0.53	0.53	0.53	8	1638	14	0	7	7	7
RFA_00427	Hammerhead_3 links to Rfam database...	0.93	0.93	0.93	14	1470	9	0	1	8	1
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	8	0	0	8	0
RFA_00434	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	8	0	0	8	0
RFA_00436	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	8	0	0	8	0
RFA_00440	Hammerhead_3 links to Rfam database...	0.31	0.40	0.25	6	1461	19	3	15	1	9
RFA_00442	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	8	0	0	8	0
RFA_00444	Hammerhead_3 links to Rfam database...	0.33	0.40	0.29	6	1519	18	6	9	3	9
RFA_00446	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	9	0	0	9	0
RFA_00449	Hammerhead_3 links to Rfam database...	0.47	0.53	0.42	8	1466	15	4	7	4	7
RFA_00582	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	5980	27	0	0	27	0
RFA_00583	Y_RNA links to Rfam database...	0.87	0.87	0.87	13	4935	27	0	2	25	2
RFA_00584	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	2911	17	0	0	17	0
RFA_00585	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	29	0	0	29	0
RFA_00586	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	3901	24	0	0	24	0
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	28	0	0	28	0
RFA_00588	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4545	27	0	0	27	0
RFA_00589	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4356	25	0	0	25	0
RFA_00594	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	2760	18	0	0	18	0
RFA_00596	Y_RNA links to Rfam database...	0.00	0.00	0.00	0	5958	49	13	24	12	15
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_00001	Bacteria_large_SRP links to Rfam database...	0.94	0.95	0.93	38	6745	11	1	2	8	2
SRP_00038	Bacteria_small_SRP links to Rfam database...	0.25	0.27	0.23	9	5011	33	1	29	3	24
SRP_00040	Bacteria_small_SRP links to Rfam database...	0.60	0.65	0.57	20	5530	26	1	14	11	11
SRP_00042	Bacteria_small_SRP links to Rfam database...	0.43	0.48	0.40	12	3975	25	1	17	7	13
SRP_00043	Bacteria_small_SRP links to Rfam database...	0.25	0.28	0.23	8	5015	34	4	23	7	21
SRP_00044	Bacteria_small_SRP links to Rfam database...	0.71	0.75	0.67	24	6069	23	0	12	11	8
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.34	0.38	0.32	12	4715	29	0	26	3	20
SRP_00051	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	5411	49	2	47	0	30
SRP_00054	Bacteria_small_SRP links to Rfam database...	0.08	0.09	0.07	3	5523	43	1	38	4	29
SRP_00057	Bacteria_small_SRP links to Rfam database...	0.49	0.54	0.45	19	6286	29	2	21	6	16
SRP_00072	Bacteria_small_SRP links to Rfam database...	0.26	0.31	0.22	9	6287	37	4	28	5	20
SRP_00074	Bacteria_small_SRP links to Rfam database...	0.23	0.28	0.21	8	6516	42	4	27	11	21
SRP_00094	Bacteria_small_SRP links to Rfam database...	0.28	0.33	0.24	8	4062	27	4	21	2	16
SRP_00095	Bacteria_small_SRP links to Rfam database...	0.02	0.04	0.03	1	3967	37	4	33	0	24
SRP_00098	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	6391	50	6	44	0	37
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.26	0.29	0.24	10	5524	32	3	28	1	24
SRP_00106	Bacteria_large_SRP links to Rfam database...	0.42	0.52	0.34	13	5215	31	8	17	6	12
SRP_00107	Bacteria_small_SRP links to Rfam database...	0.11	0.16	0.09	3	3622	34	8	22	4	16
SRP_00121	Bacteria_small_SRP links to Rfam database...	0.64	0.68	0.61	17	4250	21	0	11	10	8
SRP_00128	Bacteria_small_SRP links to Rfam database...	0.68	0.72	0.65	26	6746	23	1	13	9	10
SRP_00132	Bacteria_small_SRP links to Rfam database...	0.62	0.66	0.59	19	4819	24	0	13	11	10
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.31	0.38	0.26	11	5953	35	8	23	4	18
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_00145	Bacteria_small_SRP links to Rfam database...	0.75	0.80	0.71	32	6283	18	1	12	5	8
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.61	0.67	0.56	24	5210	24	1	18	5	12
SRP_00161	Bacteria_small_SRP links to Rfam database...	0.35	0.41	0.31	9	2821	21	4	16	1	13
SRP_00162	Bacteria_small_SRP links to Rfam database...	0.56	0.61	0.52	14	2899	19	3	10	6	9
SRP_00163	Bacteria_small_SRP links to Rfam database...	0.63	0.69	0.58	18	3455	17	2	11	4	8
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.40	0.48	0.33	12	4059	26	8	16	2	13
SRP_00194	Bacteria_small_SRP links to Rfam database...	0.68	0.71	0.65	15	3217	20	0	8	12	6
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.89	0.92	0.87	33	6865	17	1	4	12	3
SRP_00209	Bacteria_small_SRP links to Rfam database...	0.19	0.22	0.17	6	4621	37	4	25	8	21
SRP_00213	Bacteria_small_SRP links to Rfam database...	0.32	0.40	0.27	10	4149	27	8	19	0	15
SRP_00215	Bacteria_small_SRP links to Rfam database...	0.45	0.52	0.39	13	3207	21	5	15	1	12
SRP_00216	Bacteria_small_SRP links to Rfam database...	0.76	0.81	0.71	22	3372	15	1	8	6	5
SRP_00217	Bacteria_small_SRP links to Rfam database...	0.58	0.67	0.52	16	3290	18	3	12	3	8
SRP_00219	Bacteria_small_SRP links to Rfam database...	0.61	0.70	0.53	16	3291	18	3	11	4	7
SRP_00231	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	5416	44	6	38	0	34
SRP_00233	Bacteria_small_SRP links to Rfam database...	0.28	0.30	0.26	10	5113	30	0	28	2	23
SRP_00243	Bacteria_small_SRP links to Rfam database...	0.97	0.97	0.97	30	5120	14	0	1	13	1
SRP_00244	Bacteria_small_SRP links to Rfam database...	0.47	0.51	0.43	20	6857	28	4	22	2	19
SRP_00250	Bacteria_small_SRP links to Rfam database...	0.72	0.75	0.69	27	6747	21	1	11	9	9
SRP_00251	Bacteria_small_SRP links to Rfam database...	0.71	0.75	0.68	27	6981	21	1	12	8	9
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.30	0.34	0.27	10	4619	30	3	24	3	19
SRP_00269	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	5008	43	3	39	1	33
SRP_00271	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	3204	36	5	31	0	24
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.75	0.78	0.74	31	6744	18	1	10	7	9
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.77	0.79	0.75	30	6863	18	1	9	8	8
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.33	0.37	0.31	11	3705	27	2	23	2	19
SRP_00295	Bacteria_small_SRP links to Rfam database...	0.66	0.71	0.61	27	6859	22	3	14	5	11
SRP_00303	Bacteria_small_SRP links to Rfam database...	0.65	0.69	0.61	22	6634	26	1	13	12	10
SRP_00310	Bacteria_small_SRP links to Rfam database...	0.71	0.74	0.68	17	2901	15	0	8	7	6
SRP_00312	Bacteria_small_SRP links to Rfam database...	0.42	0.52	0.35	14	4146	26	6	20	0	13
SRP_00315	Bacteria_small_SRP links to Rfam database...	0.47	0.52	0.43	12	2898	20	2	14	4	11
SRP_00318	Bacteria_small_SRP links to Rfam database...	0.51	0.57	0.46	13	2975	22	0	15	7	10
SRP_00324	Bacteria_small_SRP links to Rfam database...	0.47	0.52	0.43	15	5321	25	5	15	5	14
SRP_00325	Bacteria_small_SRP links to Rfam database...	0.30	0.33	0.28	11	4332	33	1	27	5	22
SRP_00326	Bacteria_small_SRP links to Rfam database...	0.52	0.58	0.47	18	5012	23	4	16	3	13
SRP_00333	Bacteria_small_SRP links to Rfam database...	0.57	0.62	0.54	21	5112	19	5	13	1	13
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.32	0.35	0.31	11	4717	31	0	25	6	20
SRP_00342	Bacteria_small_SRP links to Rfam database...	0.72	0.76	0.68	19	3977	21	1	8	12	6
SRP_00350	Bacteria_small_SRP links to Rfam database...	0.28	0.33	0.24	9	3879	29	3	25	1	18
SRP_00356	Bacteria_small_SRP links to Rfam database...	0.38	0.43	0.33	13	5011	31	4	22	5	17
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.76	0.78	0.74	28	5318	17	1	9	7	8
SRP_00358	Bacteria_small_SRP links to Rfam database...	0.65	0.71	0.60	25	6286	24	3	14	7	10
SRP_00363	Bacteria_small_SRP links to Rfam database...	0.49	0.53	0.46	16	4718	29	1	18	10	14
SRP_00365	Bacteria_small_SRP links to Rfam database...	0.87	0.89	0.86	24	3375	11	0	4	7	3
SRP_00367	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	6736	50	6	44	0	35
SRP_00369	Bacteria_small_SRP links to Rfam database...	0.54	0.60	0.50	21	5736	31	2	19	10	14
SRP_00383	Bacteria_small_SRP links to Rfam database...	0.10	0.13	0.09	3	3208	33	3	26	4	21

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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 RNAalifold(seed) - scored higher in this pairwise comparison

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

2. Individual counts for RNAalifold(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 ]