CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MXScarna(seed)		RDfolder
MCC	0.749	>	0.487
Average MCC ± 95% Confidence Intervals	0.763 ± 0.034	>	0.458 ± 0.058
Sensitivity	0.715	>	0.421
Positive Predictive Value	0.788	>	0.571
Total TP	2095	>	1234
Total TN	367242	<	367738
Total FP	866	<	1071
Total FP CONTRA	49	<	115
Total FP INCONS	513	<	812
Total FP COMP	304	>	144
Total FN	835	<	1696
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of MXScarna(seed) and RDfolder. 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 MXScarna(seed) and RDfolder).
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 MXScarna(seed) and RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(seed) and RDfolder. 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 MXScarna(seed) and RDfolder).

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

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

Total Base Pair Counts
Total TP	2095
Total TN	367242
Total FP	866
Total FP CONTRA	49
Total FP INCONS	513
Total FP COMP	304
Total FN	835

Total Scores
MCC	0.749
Average MCC ± 95% Confidence Intervals	0.763 ± 0.034
Sensitivity	0.715
Positive Predictive Value	0.788
Nr of predictions	156

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2. Individual counts for MXScarna(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...	1.00	1.00	1.00	7	399	3	0	0	3	0
PDB_00392	tRNA links to Rfam database...	0.90	0.90	0.90	19	2829	2	0	2	0	2
PDB_00553	mir-TAR links to Rfam database...	0.90	0.82	1.00	9	456	0	0	0	0	2
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2681	21	1	19	1	23
PDB_00741	Entero_5_CRE links to Rfam database...	0.87	0.76	1.00	13	690	0	0	0	0	4
PDB_00810	s2m links to Rfam database...	0.77	0.65	0.92	11	1069	2	0	1	1	6
PDB_00828	Purine links to Rfam database...	0.82	0.67	1.00	18	2467	0	0	0	0	9
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_00876	HIV_FE links to Rfam database...	0.57	0.55	0.61	11	972	7	0	7	0	9
PDB_01001	tRNA links to Rfam database...	0.61	0.56	0.67	10	2130	6	3	2	1	8
PDB_01020	Purine links to Rfam database...	0.83	0.70	1.00	16	2262	0	0	0	0	7
PDB_01050	UnaL2 links to Rfam database...	0.78	0.62	1.00	8	622	2	0	0	2	5
PDB_01051	Telomerase-cil links to Rfam database...	0.64	0.54	0.78	7	894	5	0	2	3	6
PDB_01073	SAM links to Rfam database...	0.81	0.74	0.89	25	4343	4	1	2	1	9
PDB_01114	TPP links to Rfam database...	0.53	0.48	0.59	13	2828	11	0	9	2	14
PDB_01152	HIV_FS2 links to Rfam database...	0.85	0.79	0.92	11	549	1	0	1	0	3
RFA_00389	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00390	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00391	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00396	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00402	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00409	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00416	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	1	0	0	1	1
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...	0.97	0.93	1.00	14	1471	1	0	0	1	1
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	1	0	0	1	0
RFA_00434	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00436	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00440	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	1	0	0	1	1
RFA_00442	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00444	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1526	2	0	0	2	1
RFA_00446	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	1	0	0	1	1
RFA_00449	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	1	0	0	1	1
RFA_00583	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4935	19	0	0	19	0
RFA_00584	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	2911	11	0	0	11	0
RFA_00585	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	19	0	0	19	0
RFA_00586	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	3901	16	0	0	16	0
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	19	0	0	19	0
RFA_00588	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4545	15	0	0	15	0
RFA_00589	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4356	17	0	0	17	0
RFA_00594	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	2760	11	0	0	11	0
RFA_00632	HDV_ribozyme links to Rfam database...	0.25	0.25	0.27	7	4069	19	1	18	0	21
RFA_00636	HDV_ribozyme links to Rfam database...	0.35	0.36	0.36	10	3977	18	2	16	0	18
RFA_00642	Vimentin3 links to Rfam database...	0.56	0.50	0.64	9	2912	7	0	5	2	9
RFA_00643	Vimentin3 links to Rfam database...	0.69	0.61	0.79	11	2197	5	0	3	2	7
RFA_00644	Vimentin3 links to Rfam database...	0.69	0.61	0.79	11	2687	5	0	3	2	7
RFA_00645	Vimentin3 links to Rfam database...	0.30	0.28	0.33	5	2400	11	0	10	1	13
RFA_00649	Vimentin3 links to Rfam database...	0.73	0.67	0.80	12	2130	5	0	3	2	6
RFA_00651	Vimentin3 links to Rfam database...	0.73	0.67	0.80	12	2065	5	0	3	2	6
RFA_00653	Vimentin3 links to Rfam database...	0.67	0.61	0.73	11	2130	6	0	4	2	7
RFA_00654	Vimentin3 links to Rfam database...	0.73	0.67	0.80	12	2400	5	0	3	2	6
RFA_00658	Hammerhead_1 links to Rfam database...	0.61	0.57	0.67	8	1116	5	0	4	1	6
RFA_00659	Hammerhead_1 links to Rfam database...	0.46	0.43	0.50	6	1116	7	0	6	1	8
RFA_00664	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00667	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00668	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00672	Hammerhead_1 links to Rfam database...	0.72	0.69	0.75	9	891	4	0	3	1	4
RFA_00673	Hammerhead_1 links to Rfam database...	0.61	0.57	0.67	8	1116	5	0	4	1	6
RFA_00674	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	1116	4	0	3	1	5
RFA_00675	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00677	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00678	Hammerhead_1 links to Rfam database...	0.66	0.64	0.69	9	933	5	0	4	1	5
RFA_00680	Hammerhead_1 links to Rfam database...	0.61	0.57	0.67	8	1116	5	0	4	1	6
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...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00703	Hammerhead_1 links to Rfam database...	0.62	0.57	0.67	8	4266	8	1	3	4	6
RFA_00704	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00705	Hammerhead_1 links to Rfam database...	0.66	0.64	0.69	9	1022	5	0	4	1	5
RFA_00706	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	1023	4	0	3	1	5
RFA_00707	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	1023	4	0	3	1	5
RFA_00708	Hammerhead_1 links to Rfam database...	0.64	0.57	0.73	8	1024	4	0	3	1	6
RFA_00709	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00710	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00711	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	1023	4	0	3	1	5
RFA_00715	Hammerhead_1 links to Rfam database...	0.56	0.50	0.64	7	935	5	0	4	1	7
RFA_00716	Hammerhead_1 links to Rfam database...	0.48	0.43	0.55	6	935	6	0	5	1	8
RFA_00717	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	891	3	0	3	0	5
RFA_00730	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00731	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00733	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00734	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00736	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00737	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00745	s2m links to Rfam database...	1.00	1.00	1.00	12	934	1	0	0	1	0
RFA_00749	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00758	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00762	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00763	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00764	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00765	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00767	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1875	6	2	4	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1875	6	2	4	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.57	0.56	0.59	10	1999	7	2	5	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.57	0.56	0.59	10	1936	7	2	5	0	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...	0.30	0.31	0.29	5	2128	12	1	11	0	11
SPR_00020	tRNA links to Rfam database...	0.97	0.95	1.00	19	2682	1	0	0	1	1
SPR_00023	tRNA links to Rfam database...	0.77	0.71	0.83	15	2832	4	0	3	1	6
SPR_00064	tRNA links to Rfam database...	0.98	0.95	1.00	20	2830	0	0	0	0	1
SPR_00111	tRNA links to Rfam database...	0.98	0.95	1.00	20	2681	0	0	0	0	1
SPR_00113	tRNA links to Rfam database...	0.31	0.25	0.38	5	2762	9	0	8	1	15
SPR_00137	tRNA links to Rfam database...	0.82	0.76	0.89	16	2908	4	0	2	2	5
SPR_00273	tRNA links to Rfam database...	0.58	0.57	0.60	12	2830	8	0	8	0	9
SPR_00277	tRNA links to Rfam database...	0.98	0.95	1.00	20	2906	0	0	0	0	1
SPR_00279	tRNA links to Rfam database...	0.95	0.90	1.00	19	2907	1	0	0	1	2
SPR_00314	tRNA links to Rfam database...	1.00	1.00	1.00	21	2905	0	0	0	0	0
SPR_00394	tRNA links to Rfam database...	0.73	0.71	0.75	15	3635	5	0	5	0	6
SPR_00402	tRNA links to Rfam database...	0.98	0.95	1.00	20	2536	0	0	0	0	1
SPR_00434	tRNA links to Rfam database...	0.98	0.95	1.00	20	2830	0	0	0	0	1
SPR_00452	tRNA links to Rfam database...	0.98	0.95	1.00	20	2830	0	0	0	0	1
SPR_00595	tRNA links to Rfam database...	0.98	0.95	1.00	20	2755	0	0	0	0	1
SPR_00721	tRNA links to Rfam database...	0.98	0.95	1.00	20	2906	0	0	0	0	1
SPR_00816	tRNA links to Rfam database...	0.52	0.50	0.56	10	3468	9	0	8	1	10
SPR_00867	tRNA links to Rfam database...	0.98	0.95	1.00	20	2906	0	0	0	0	1
SPR_00912	tRNA links to Rfam database...	1.00	1.00	1.00	21	2982	0	0	0	0	0
SPR_01157	tRNA links to Rfam database...	0.98	0.95	1.00	20	2755	0	0	0	0	1
SRP_00008	Bacteria_small_SRP links to Rfam database...	0.55	0.52	0.59	13	2904	10	0	9	1	12
SRP_00042	Bacteria_small_SRP links to Rfam database...	0.54	0.52	0.57	13	3982	13	1	9	3	12
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.95	0.94	0.97	30	4722	3	0	1	2	2
SRP_00094	Bacteria_small_SRP links to Rfam database...	0.62	0.58	0.67	14	4074	12	1	6	5	10
SRP_00095	Bacteria_small_SRP links to Rfam database...	0.65	0.60	0.71	15	3984	10	1	5	4	10
SRP_00107	Bacteria_small_SRP links to Rfam database...	0.26	0.26	0.26	5	3636	16	2	12	2	14
SRP_00121	Bacteria_small_SRP links to Rfam database...	0.60	0.64	0.57	16	4250	13	4	8	1	9
SRP_00132	Bacteria_small_SRP links to Rfam database...	0.63	0.62	0.64	18	4823	14	0	10	4	11
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.60	0.64	0.57	16	4158	13	3	9	1	9
SRP_00161	Bacteria_small_SRP links to Rfam database...	0.84	0.86	0.83	19	2827	6	0	4	2	3
SRP_00162	Bacteria_small_SRP links to Rfam database...	0.89	0.91	0.88	21	2902	5	0	3	2	2
SRP_00163	Bacteria_small_SRP links to Rfam database...	0.87	0.88	0.85	23	3459	6	0	4	2	3
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.51	0.48	0.55	12	4073	14	1	9	4	13
SRP_00194	Bacteria_small_SRP links to Rfam database...	0.74	0.76	0.73	16	3218	9	0	6	3	5
SRP_00209	Bacteria_small_SRP links to Rfam database...	0.43	0.41	0.46	11	4632	15	1	12	2	16
SRP_00213	Bacteria_small_SRP links to Rfam database...	0.66	0.56	0.78	14	4168	9	1	3	5	11
SRP_00215	Bacteria_small_SRP links to Rfam database...	0.88	0.88	0.88	22	3215	4	0	3	1	3
SRP_00216	Bacteria_small_SRP links to Rfam database...	0.76	0.70	0.83	19	3380	6	1	3	2	8
SRP_00217	Bacteria_small_SRP links to Rfam database...	0.74	0.71	0.77	17	3299	7	0	5	2	7
SRP_00219	Bacteria_small_SRP links to Rfam database...	0.82	0.83	0.83	19	3298	7	0	4	3	4
SRP_00222	Bacteria_small_SRP links to Rfam database...	0.83	0.76	0.90	19	3060	4	1	1	2	6
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.57	0.59	0.57	17	4626	14	2	11	1	12
SRP_00268	Bacteria_small_SRP links to Rfam database...	0.57	0.56	0.60	15	4161	12	1	9	2	12
SRP_00270	Bacteria_small_SRP links to Rfam database...	0.93	0.87	1.00	27	4629	4	0	0	4	4
SRP_00271	Bacteria_small_SRP links to Rfam database...	0.57	0.50	0.67	12	3222	6	0	6	0	12
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.86	0.80	0.92	24	3715	3	0	2	1	6
SRP_00310	Bacteria_small_SRP links to Rfam database...	0.76	0.78	0.75	18	2902	7	0	6	1	5
SRP_00312	Bacteria_small_SRP links to Rfam database...	0.44	0.41	0.48	11	4163	15	1	11	3	16
SRP_00315	Bacteria_small_SRP links to Rfam database...	0.75	0.78	0.72	18	2901	7	0	7	0	5
SRP_00318	Bacteria_small_SRP links to Rfam database...	0.71	0.70	0.73	16	2981	6	0	6	0	7
SRP_00325	Bacteria_small_SRP links to Rfam database...	0.92	0.85	1.00	28	4343	2	0	0	2	5
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.46	0.45	0.47	14	4723	16	0	16	0	17
SRP_00342	Bacteria_small_SRP links to Rfam database...	0.71	0.68	0.74	17	3982	8	1	5	2	8
SRP_00350	Bacteria_small_SRP links to Rfam database...	0.37	0.33	0.43	9	3895	14	1	11	2	18
SRP_00363	Bacteria_small_SRP links to Rfam database...	0.91	0.90	0.93	27	4724	6	0	2	4	3
SRP_00365	Bacteria_small_SRP links to Rfam database...	0.82	0.74	0.91	20	3381	4	0	2	2	7
SRP_00383	Bacteria_small_SRP links to Rfam database...	0.75	0.67	0.84	16	3221	5	0	3	2	8

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Performance of RDfolder - scored lower in this pairwise comparison

1. Total counts & total scores for RDfolder

Total Base Pair Counts
Total TP	1234
Total TN	367738
Total FP	1071
Total FP CONTRA	115
Total FP INCONS	812
Total FP COMP	144
Total FN	1696

Total Scores
MCC	0.487
Average MCC ± 95% Confidence Intervals	0.458 ± 0.058
Sensitivity	0.421
Positive Predictive Value	0.571
Nr of predictions	156

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2. Individual counts for RDfolder [ 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_00392	tRNA links to Rfam database...	0.53	0.48	0.59	10	2833	7	2	5	0	11
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	2684	18	1	16	1	23
PDB_00741	Entero_5_CRE links to Rfam database...	0.84	0.71	1.00	12	691	0	0	0	0	5
PDB_00810	s2m links to Rfam database...	-0.01	0.00	0.00	0	1078	3	0	3	0	17
PDB_00828	Purine links to Rfam database...	0.88	0.78	1.00	21	2464	0	0	0	0	6
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_00876	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
PDB_01001	tRNA links to Rfam database...	0.39	0.28	0.56	5	2136	4	0	4	0	13
PDB_01020	Purine links to Rfam database...	0.86	0.74	1.00	17	2261	1	0	0	1	6
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	5	0	1	4	4
PDB_01073	SAM links to Rfam database...	0.43	0.38	0.50	13	4345	13	1	12	0	21
PDB_01114	TPP links to Rfam database...	0.27	0.22	0.35	6	2833	11	1	10	0	21
PDB_01152	HIV_FS2 links to Rfam database...	0.88	0.79	1.00	11	550	0	0	0	0	3
RFA_00389	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	1	0	0	1	0
RFA_00390	Hammerhead_3 links to Rfam database...	0.33	0.33	0.33	5	1416	10	1	9	0	10
RFA_00391	Hammerhead_3 links to Rfam database...	0.51	0.27	1.00	4	1427	1	0	0	1	11
RFA_00396	Hammerhead_3 links to Rfam database...	0.63	0.40	1.00	6	1425	0	0	0	0	9
RFA_00402	Hammerhead_3 links to Rfam database...	0.40	0.33	0.50	5	1421	5	0	5	0	10
RFA_00409	Hammerhead_3 links to Rfam database...	0.77	0.60	1.00	9	1422	1	0	0	1	6
RFA_00416	Hammerhead_3 links to Rfam database...	0.77	0.60	1.00	9	1476	1	0	0	1	6
RFA_00425	Hammerhead_3 links to Rfam database...	0.66	0.67	0.67	10	1638	6	1	4	1	5
RFA_00427	Hammerhead_3 links to Rfam database...	0.38	0.33	0.45	5	1474	6	1	5	0	10
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00434	Hammerhead_3 links to Rfam database...	0.39	0.40	0.40	6	1416	10	3	6	1	9
RFA_00436	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00440	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	2	0	0	2	0
RFA_00442	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00444	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1525	1	0	0	1	0
RFA_00446	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	2	0	0	2	1
RFA_00449	Hammerhead_3 links to Rfam database...	0.58	0.33	1.00	5	1480	1	0	0	1	10
RFA_00583	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4935	10	0	0	10	0
RFA_00584	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	2911	7	0	0	7	0
RFA_00585	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	11	0	0	11	0
RFA_00586	Y_RNA links to Rfam database...	0.00	0.00	0.00	0	3910	6	0	6	0	15
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	11	0	0	11	0
RFA_00588	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4545	13	0	0	13	0
RFA_00589	Y_RNA links to Rfam database...	0.97	0.93	1.00	14	4357	14	0	0	14	1
RFA_00594	Y_RNA links to Rfam database...	0.90	0.87	0.93	13	2761	7	0	1	6	2
RFA_00632	HDV_ribozyme links to Rfam database...	0.62	0.54	0.71	15	4074	6	1	5	0	13
RFA_00636	HDV_ribozyme links to Rfam database...	0.65	0.64	0.67	18	3978	9	3	6	0	10
RFA_00642	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2917	9	3	6	0	18
RFA_00643	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2205	6	0	6	0	18
RFA_00644	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2694	7	3	4	0	18
RFA_00645	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2410	5	1	4	0	18
RFA_00649	Vimentin3 links to Rfam database...	0.53	0.33	0.86	6	2138	1	0	1	0	12
RFA_00651	Vimentin3 links to Rfam database...	0.39	0.33	0.46	6	2067	7	0	7	0	12
RFA_00653	Vimentin3 links to Rfam database...	0.35	0.33	0.38	6	2129	10	2	8	0	12
RFA_00654	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2404	11	2	9	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	10	0	10	0	14
RFA_00667	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	982	8	1	7	0	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	897	6	0	6	0	13
RFA_00673	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1125	3	0	3	0	14
RFA_00674	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1122	6	0	6	0	14
RFA_00675	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	985	5	0	5	0	14
RFA_00677	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	984	6	0	6	0	14
RFA_00678	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	941	5	0	5	0	14
RFA_00680	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1121	7	2	5	0	14
RFA_00684	Hammerhead_1 links to Rfam database...	0.53	0.29	1.00	4	986	1	0	0	1	10
RFA_00685	Hammerhead_1 links to Rfam database...	0.47	0.36	0.63	5	982	4	0	3	1	9
RFA_00703	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	4269	9	4	5	0	14
RFA_00704	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	983	7	0	7	0	14
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...	-0.01	0.00	0.00	0	1027	8	0	8	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...	-0.01	0.00	0.00	0	1028	7	0	7	0	14
RFA_00709	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	982	8	0	8	0	14
RFA_00710	Hammerhead_1 links to Rfam database...	0.42	0.36	0.50	5	980	6	0	5	1	9
RFA_00711	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1023	12	0	12	0	14
RFA_00715	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	940	6	0	6	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...	-0.01	0.00	0.00	0	898	5	0	5	0	14
RFA_00730	s2m links to Rfam database...	-0.01	0.00	0.00	0	897	6	1	5	0	12
RFA_00731	s2m links to Rfam database...	0.41	0.42	0.42	5	891	8	3	4	1	7
RFA_00733	s2m links to Rfam database...	-0.01	0.00	0.00	0	898	5	0	5	0	12
RFA_00734	s2m links to Rfam database...	0.67	0.58	0.78	7	894	3	0	2	1	5
RFA_00736	s2m links to Rfam database...	0.43	0.42	0.45	5	892	7	1	5	1	7
RFA_00737	s2m links to Rfam database...	0.43	0.42	0.45	5	892	7	2	4	1	7
RFA_00745	s2m links to Rfam database...	-0.01	0.00	0.00	0	938	8	2	6	0	12
RFA_00749	s2m links to Rfam database...	0.43	0.42	0.45	5	892	7	1	5	1	7
RFA_00758	s2m links to Rfam database...	-0.01	0.00	0.00	0	900	3	0	3	0	12
RFA_00762	s2m links to Rfam database...	-0.01	0.00	0.00	0	894	9	2	7	0	12
RFA_00763	s2m links to Rfam database...	-0.01	0.00	0.00	0	897	6	1	5	0	12
RFA_00764	s2m links to Rfam database...	0.51	0.42	0.63	5	895	4	1	2	1	7
RFA_00765	s2m links to Rfam database...	0.43	0.42	0.45	5	892	7	2	4	1	7
RFA_00767	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	1882	0	0	0	0	9
RFA_00768	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	0	0	0	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.50	0.50	0.50	9	1935	9	4	5	0	9
RFA_00770	Corona_pk3 links to Rfam database...	0.47	0.39	0.58	7	2004	5	1	4	0	11
RFA_00773	Corona_pk3 links to Rfam database...	0.67	0.50	0.90	9	1943	1	1	0	0	9
RFA_00779	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	1944	0	0	0	0	9
RFA_00808	RydC links to Rfam database...	0.68	0.56	0.82	9	2005	3	0	2	1	7
RFA_00809	RydC links to Rfam database...	0.40	0.38	0.43	6	2131	8	1	7	0	10
SPR_00020	tRNA links to Rfam database...	0.54	0.45	0.64	9	2687	8	0	5	3	11
SPR_00023	tRNA links to Rfam database...	0.82	0.86	0.78	18	2827	5	0	5	0	3
SPR_00064	tRNA links to Rfam database...	0.60	0.57	0.63	12	2831	7	0	7	0	9
SPR_00111	tRNA links to Rfam database...	0.48	0.48	0.50	10	2681	11	3	7	1	11
SPR_00113	tRNA links to Rfam database...	0.92	0.85	1.00	17	2758	1	0	0	1	3
SPR_00137	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2908	18	1	17	0	21
SPR_00273	tRNA links to Rfam database...	0.95	0.90	1.00	19	2831	0	0	0	0	2
SPR_00277	tRNA links to Rfam database...	0.98	0.95	1.00	20	2906	0	0	0	0	1
SPR_00279	tRNA links to Rfam database...	0.44	0.19	1.00	4	2922	0	0	0	0	17
SPR_00314	tRNA links to Rfam database...	0.98	0.95	1.00	20	2906	1	0	0	1	1
SPR_00394	tRNA links to Rfam database...	0.44	0.24	0.83	5	3649	1	0	1	0	16
SPR_00402	tRNA links to Rfam database...	0.98	0.95	1.00	20	2536	1	0	0	1	1
SPR_00434	tRNA links to Rfam database...	0.98	0.95	1.00	20	2830	0	0	0	0	1
SPR_00452	tRNA links to Rfam database...	0.46	0.43	0.50	9	2832	9	0	9	0	12
SPR_00595	tRNA links to Rfam database...	0.98	0.95	1.00	20	2755	0	0	0	0	1
SPR_00721	tRNA links to Rfam database...	0.98	0.95	1.00	20	2906	1	0	0	1	1
SPR_00816	tRNA links to Rfam database...	0.33	0.35	0.32	7	3464	16	2	13	1	13
SPR_00867	tRNA links to Rfam database...	0.25	0.24	0.26	5	2907	14	2	12	0	16
SPR_00912	tRNA links to Rfam database...	1.00	1.00	1.00	21	2982	2	0	0	2	0
SPR_01157	tRNA links to Rfam database...	0.81	0.81	0.81	17	2754	5	3	1	1	4
SRP_00008	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	2910	17	0	16	1	25
SRP_00042	Bacteria_small_SRP links to Rfam database...	0.50	0.48	0.52	12	3982	12	0	11	1	13
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.60	0.53	0.68	17	4728	9	0	8	1	15
SRP_00094	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	4076	19	3	16	0	24
SRP_00095	Bacteria_small_SRP links to Rfam database...	0.28	0.28	0.29	7	3981	17	3	14	0	18
SRP_00107	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	3632	25	6	17	2	19
SRP_00121	Bacteria_small_SRP links to Rfam database...	0.50	0.44	0.58	11	4259	8	1	7	0	14
SRP_00132	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	4827	25	2	22	1	29
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.38	0.40	0.37	10	4159	17	8	9	0	15
SRP_00161	Bacteria_small_SRP links to Rfam database...	0.55	0.41	0.75	9	2838	3	0	3	0	13
SRP_00162	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	2911	15	1	14	0	23
SRP_00163	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	3472	14	0	14	0	26
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.40	0.32	0.50	8	4079	9	3	5	1	17
SRP_00194	Bacteria_small_SRP links to Rfam database...	0.50	0.43	0.60	9	3225	6	0	6	0	12
SRP_00209	Bacteria_small_SRP links to Rfam database...	0.57	0.56	0.60	15	4631	10	2	8	0	12
SRP_00213	Bacteria_small_SRP links to Rfam database...	0.41	0.40	0.43	10	4163	13	3	10	0	15
SRP_00215	Bacteria_small_SRP links to Rfam database...	0.63	0.52	0.76	13	3223	4	0	4	0	12
SRP_00216	Bacteria_small_SRP links to Rfam database...	0.91	0.89	0.92	24	3377	3	1	1	1	3
SRP_00217	Bacteria_small_SRP links to Rfam database...	0.31	0.25	0.40	6	3306	10	0	9	1	18
SRP_00219	Bacteria_small_SRP links to Rfam database...	0.78	0.78	0.78	18	3298	6	0	5	1	5
SRP_00222	Bacteria_small_SRP links to Rfam database...	0.54	0.52	0.57	13	3058	11	2	8	1	12
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.48	0.31	0.75	9	4644	4	0	3	1	20
SRP_00268	Bacteria_small_SRP links to Rfam database...	0.37	0.37	0.38	10	4160	16	2	14	0	17
SRP_00270	Bacteria_small_SRP links to Rfam database...	0.47	0.45	0.50	14	4628	14	3	11	0	17
SRP_00271	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	3220	20	1	19	0	24
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.45	0.40	0.52	12	3718	11	0	11	0	18
SRP_00310	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	2921	5	1	4	0	23
SRP_00312	Bacteria_small_SRP links to Rfam database...	0.87	0.85	0.88	23	4160	3	0	3	0	4
SRP_00315	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	2912	14	0	14	0	23
SRP_00318	Bacteria_small_SRP links to Rfam database...	0.16	0.13	0.21	3	2989	11	1	10	0	20
SRP_00325	Bacteria_small_SRP links to Rfam database...	0.45	0.39	0.52	13	4346	12	1	11	0	20
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.33	0.29	0.38	9	4729	15	0	15	0	22
SRP_00342	Bacteria_small_SRP links to Rfam database...	0.51	0.48	0.55	12	3983	10	2	8	0	13
SRP_00350	Bacteria_small_SRP links to Rfam database...	0.82	0.78	0.88	21	3892	4	0	3	1	6
SRP_00363	Bacteria_small_SRP links to Rfam database...	0.41	0.30	0.56	9	4737	9	1	6	2	21
SRP_00365	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	3388	15	1	14	0	27
SRP_00383	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	3223	17	0	17	0	24

^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 MXScarna(seed) - scored higher in this pairwise comparison

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

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

Performance of RDfolder - scored lower in this pairwise comparison

1. Total counts & total scores for RDfolder

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